X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4
Temperature 277.0
Details 30-33% PEG-400, 200 mM magnesium chloride, 100 mM potassium chloride, 25 mM sodium citrate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 140.24 α = 90
b = 143.2 β = 90
c = 180.05 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 RAYONIX MX300HE -- 2015-02-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-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
3 50 97.8 0.201 -- 12.906 10.1 -- 68041 -- -- --
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)
3.0 3.11 85.4 -- -- -- 5.8 5864

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 3.04 50.0 -- 0.0 -- 64544 3426 96.79 -- 0.2615 0.2603 0.2826 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 3.042 3.121 -- 184 3585 0.376 0.442 -- 73.92
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 120.798
Anisotropic B[1][1] 12.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -10.89
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.03
RMS Deviations
Key Refinement Restraint Deviation
r_chiral_restr 0.06
r_mcbond_other 2.662
r_angle_refined_deg 1.06
r_dihedral_angle_4_deg 13.981
r_bond_refined_d 0.006
r_dihedral_angle_3_deg 16.136
r_gen_planes_other 0.001
r_bond_other_d 0.001
r_mcangle_it 4.469
r_mcbond_it 2.665
r_angle_other_deg 0.708
r_dihedral_angle_2_deg 35.33
r_gen_planes_refined 0.004
r_dihedral_angle_1_deg 5.869
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13317
Nucleic Acid Atoms 0
Heterogen Atoms 223
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0073
SCALEPACK data scaling version: 0.98
PDB_EXTRACT data extraction version: 3.15
PHASER phasing version: 2.5.6