X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 291.0
Details 0.2 M ammonium citrate tribasic pH 7.0, 20 PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 105.54 α = 90
b = 105.54 β = 90
c = 114.68 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r mirrors 2009-04-13
Diffraction Radiation
Monochromator Protocol
double crystal monochromator SAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.9793 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
2 48.6 99.8 -- 0.118 -- 11.7 50248 50248 0.0 0.0 25.2
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)
2.0 2.03 97.2 -- 0.822 3.15 7.4 2398

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
SAD 2.0 48.574 -- 0.0 50212 50212 2006 99.62 0.148 0.148 0.142 0.188 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 1.9995 2.0495 3389 135 3254 0.2383 0.3324 -- 92.0
X Ray Diffraction 2.0495 2.1049 3566 141 3425 0.2171 0.2774 -- 96.0
X Ray Diffraction 2.1049 2.1669 3551 142 3409 0.1917 0.2434 -- 96.0
X Ray Diffraction 2.1669 2.2368 3549 139 3410 0.1836 0.2295 -- 96.0
X Ray Diffraction 2.2368 2.3167 3545 138 3407 0.1779 0.2275 -- 96.0
X Ray Diffraction 2.3167 2.4095 3593 146 3447 0.1717 0.2123 -- 96.0
X Ray Diffraction 2.4095 2.5191 3561 139 3422 0.1699 0.2424 -- 96.0
X Ray Diffraction 2.5191 2.6519 3572 145 3427 0.1701 0.2038 -- 96.0
X Ray Diffraction 2.6519 2.8181 3584 142 3442 0.1582 0.1938 -- 96.0
X Ray Diffraction 2.8181 3.0356 3605 146 3459 0.1531 0.1945 -- 96.0
X Ray Diffraction 3.0356 3.341 3601 146 3455 0.1433 0.2241 -- 96.0
X Ray Diffraction 3.341 3.8241 3636 143 3493 0.1207 0.1529 -- 96.0
X Ray Diffraction 3.8241 4.8169 3652 147 3505 0.1035 0.1567 -- 96.0
X Ray Diffraction 4.8169 42.4642 3793 152 3641 0.1208 0.152 -- 96.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model mixed
RMS Deviations
Key Refinement Restraint Deviation
f_plane_restr 0.003
f_chiral_restr 0.054
f_dihedral_angle_d 15.461
f_angle_d 0.803
f_bond_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4442
Nucleic Acid Atoms 0
Heterogen Atoms 30
Solvent Atoms 341

Software

Computing
Computing Package Purpose
SBCCOLLECT, HKL3000 Data Collection
HKL-3000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
HKL3000, SHELXD,MLPHARE,DM,RESOLVE,COOT Structure Solution
PHENIX (phenix.refine: 1.8.1_1161) Structure Refinement
Software
Software Name Purpose
PHENIX version: (phenix.refine: 1.8.1_1161) refinement
COOT model building
RESOLVE model building
DM model building
MLPHARE model building
SHELXD model building
HKL3000 model building
HKL3000 data collection
SBCCOLLECT data collection