X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 298.0
Details 100mM Bis Tris pH 5.5, 25% PEG 3350, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 35.34 α = 90
b = 41.22 β = 90
c = 46.6 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 RIGAKU SATURN 944+ -- 2010-10-13
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF 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
2.03 30.87 98.6 -- 0.064 -- 5.7 4685 4685 -- -- --
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)
2.028 2.14 90.7 0.196 0.196 3.9 3.8 605

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
-- 2.03 23.3 -- 0.0 -- 4649 212 98.3 -- 0.19 0.187 0.253 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 2.03 2.08 -- 14 275 0.205 0.35 -- 81.18
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 18.35
Anisotropic B[1][1] 0.39
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.45
RMS Deviations
Key Refinement Restraint Deviation
r_mcbond_it 1.534
r_bond_refined_d 0.012
r_scangle_it 6.29
r_mcbond_other 0.412
r_bond_other_d 0.0
r_gen_planes_other 0.003
r_angle_refined_deg 1.225
r_chiral_restr 0.081
r_dihedral_angle_3_deg 17.085
r_dihedral_angle_1_deg 10.208
r_scbond_it 4.282
r_angle_other_deg 0.649
r_mcangle_it 2.607
r_gen_planes_refined 0.01
r_dihedral_angle_2_deg 42.904
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 576
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 67

Software

Software
Software Name Purpose
SCALA data scaling version: 3.3.16
PHASER phasing version: 2.1.4
REFMAC refinement
PDB_EXTRACT data extraction version: 3.10
XSCALE data scaling