X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.5
Temperature 293.0
Details 25% PEG 3350, 0.1 M Citric acid pH 3.5, 2 mM ZnCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.66 α = 90
b = 79.66 β = 90
c = 79.66 γ = 90
Symmetry
Space Group P 21 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV -- 2007-05-30
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ DW 1.5418 -- --

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
2.26 50 100.0 0.105 0.07 -- 18.3 8156 8156 0.0 0.0 53.2
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)
2.26 2.34 99.9 0.8958 0.7177 1.57 6.8 --

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 2.26 39.84 -- -- 8159 8156 376 99.96 -- 0.20664 0.20405 0.25746 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 2.26 2.319 -- 29 573 0.276 0.365 -- 99.83
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 45.102
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.121
r_scangle_it 4.695
r_bond_refined_d 0.021
r_scbond_it 3.047
r_dihedral_angle_1_deg 8.023
r_mcangle_it 1.94
r_symmetry_hbond_refined 0.22
r_chiral_restr 0.123
r_nbtor_refined 0.308
r_xyhbond_nbd_refined 0.162
r_nbd_refined 0.217
r_dihedral_angle_3_deg 19.282
r_dihedral_angle_4_deg 12.583
r_dihedral_angle_2_deg 36.39
r_gen_planes_refined 0.007
r_symmetry_vdw_refined 0.207
r_angle_refined_deg 1.835
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1138
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 40

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
PHASER phasing
REFMAC refinement
PDB_EXTRACT data extraction version: 3.000