X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 289.0
Details B11: 0.2 M lithium sulfate, 0.1 M Bis-TrisHCl pH 6.5, 25 %(w/v) PEG 3350, 5 mM CdCl2, 100mM ampicillin, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 39 α = 90
b = 78.7 β = 90
c = 134.38 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2011-10-09
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.5 50 98.2 -- 0.096 -- 6.2 -- 123712 0.0 0.0 13.0
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.5 1.53 93.5 -- 0.782 2.1 4.1 3509

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
MOLECULAR REPLACEMENT 1.5 34.942 -- 0.0 123712 123712 6300 96.72 0.137 0.137 0.137 0.149 random
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.5 1.5171 3569 225 3344 0.2355 0.255 -- 84.0
X Ray Diffraction 1.5171 1.5349 3814 208 3606 0.221 0.2277 -- 90.0
X Ray Diffraction 1.5349 1.5537 3920 195 3725 0.1975 0.2067 -- 91.0
X Ray Diffraction 1.5537 1.5733 3961 184 3777 0.1844 0.1901 -- 93.0
X Ray Diffraction 1.5733 1.594 4021 154 3867 0.173 0.199 -- 96.0
X Ray Diffraction 1.594 1.6159 4057 200 3857 0.165 0.1892 -- 94.0
X Ray Diffraction 1.6159 1.6389 4036 215 3821 0.1541 0.1457 -- 95.0
X Ray Diffraction 1.6389 1.6634 4129 237 3892 0.1499 0.1702 -- 97.0
X Ray Diffraction 1.6634 1.6894 4101 195 3906 0.1483 0.1942 -- 95.0
X Ray Diffraction 1.6894 1.7171 4010 181 3829 0.1466 0.1449 -- 96.0
X Ray Diffraction 1.7171 1.7467 4142 195 3947 0.143 0.1942 -- 97.0
X Ray Diffraction 1.7467 1.7785 4130 233 3897 0.1328 0.1666 -- 96.0
X Ray Diffraction 1.7785 1.8127 4136 186 3950 0.129 0.1606 -- 98.0
X Ray Diffraction 1.8127 1.8497 4187 234 3953 0.1274 0.1421 -- 97.0
X Ray Diffraction 1.8497 1.8899 4149 208 3941 0.1339 0.1352 -- 98.0
X Ray Diffraction 1.8899 1.9338 4164 207 3957 0.135 0.1483 -- 97.0
X Ray Diffraction 1.9338 1.9822 4206 229 3977 0.1294 0.1443 -- 99.0
X Ray Diffraction 1.9822 2.0358 4206 202 4004 0.1229 0.1404 -- 99.0
X Ray Diffraction 2.0358 2.0957 4190 198 3992 0.1294 0.1449 -- 99.0
X Ray Diffraction 2.0957 2.1633 4262 226 4036 0.122 0.1429 -- 99.0
X Ray Diffraction 2.1633 2.2406 4194 282 3912 0.1217 0.1118 -- 99.0
X Ray Diffraction 2.2406 2.3303 4223 228 3995 0.1257 0.1293 -- 99.0
X Ray Diffraction 2.3303 2.4363 4272 210 4062 0.1306 0.1311 -- 100.0
X Ray Diffraction 2.4363 2.5648 4228 218 4010 0.134 0.1626 -- 99.0
X Ray Diffraction 2.5648 2.7254 4235 205 4030 0.1368 0.1405 -- 99.0
X Ray Diffraction 2.7254 2.9357 4244 208 4036 0.1389 0.1723 -- 100.0
X Ray Diffraction 2.9357 3.231 4264 211 4053 0.1365 0.1366 -- 100.0
X Ray Diffraction 3.231 3.698 4221 232 3989 0.1249 0.1573 -- 99.0
X Ray Diffraction 3.698 4.6574 4238 196 4042 0.1197 0.1284 -- 100.0
X Ray Diffraction 4.6574 34.9519 4203 198 4005 0.1475 0.143 -- 98.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed
Mean Isotropic B 18.9
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.007
f_chiral_restr 0.097
f_dihedral_angle_d 14.268
f_angle_d 1.581
f_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3557
Nucleic Acid Atoms 0
Heterogen Atoms 52
Solvent Atoms 469

Software

Computing
Computing Package Purpose
SBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-3000 Data Reduction (data scaling)
HKL3000, Molrep Structure Solution
PHENIX (phenix.refine: 1.8.1_1161) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1161) refinement
Molrep model building
HKL3000 model building
HKL3000 data collection
SBCCOLLECT data collection