X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Hanging Drop
pH 5.5
Temperature 298.0
Details 25% PEG3350, 0.2M LiCl, 5% acetone, pH 5.5, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 60.59 α = 90
b = 62.42 β = 90
c = 96.07 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 315 -- 2009-10-27
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.964 Photon Factory BL-17A

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
1.99 50 99.9 0.068 -- -- 3.7 -- 25298 -- -- --
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)
1.99 2.02 98.9 0.243 -- -- 3.4 2455

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 2.0 50.0 -- 0.0 25298 24896 1060 98.4 -- -- 0.188 0.221 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 2.0 2.03 -- -- 798 0.241 -- -- --
X Ray Diffraction 2.03 2.07 -- -- 1180 0.233 -- -- --
X Ray Diffraction 2.07 2.11 -- 9 1177 0.223 0.293 -- --
X Ray Diffraction 2.11 2.15 -- 53 1123 0.194 0.242 -- --
X Ray Diffraction 2.15 2.19 -- 53 1139 0.198 0.269 -- --
X Ray Diffraction 2.19 2.24 -- 53 1149 0.169 0.236 -- --
X Ray Diffraction 2.24 2.29 -- 61 1110 0.201 0.254 -- --
X Ray Diffraction 2.29 2.35 -- 58 1140 0.172 0.221 -- --
X Ray Diffraction 2.35 2.41 -- 57 1130 0.175 0.243 -- --
X Ray Diffraction 2.41 2.48 -- 62 1123 0.201 0.248 -- --
X Ray Diffraction 2.48 2.56 -- 41 1154 0.19 0.236 -- --
X Ray Diffraction 2.56 2.65 -- 57 1135 0.193 0.229 -- --
X Ray Diffraction 2.65 2.76 -- 62 1138 0.184 0.251 -- --
X Ray Diffraction 2.76 2.88 -- 70 1127 0.208 0.304 -- --
X Ray Diffraction 2.88 3.04 -- 62 1141 0.215 0.248 -- --
X Ray Diffraction 3.04 3.23 -- 55 1154 0.176 0.181 -- --
X Ray Diffraction 3.23 3.48 -- 65 1155 0.201 0.248 -- --
X Ray Diffraction 3.48 3.83 -- 43 1169 0.179 0.23 -- --
X Ray Diffraction 3.83 4.38 -- 65 1167 0.16 0.172 -- --
X Ray Diffraction 4.38 5.52 -- 65 1178 0.139 0.149 -- --
X Ray Diffraction 5.52 50.0 -- 69 1249 0.233 0.231 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.775
Anisotropic B[1][1] 8.96
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.11
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -7.85
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.005
c_angle_deg 1.428
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.26
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2414
Nucleic Acid Atoms 0
Heterogen Atoms 75
Solvent Atoms 264

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
CNS refinement
PDB_EXTRACT data extraction version: 3.004
ADSC data collection version: Quantum