X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 289.0
Details 18% PEG 5000 MME, 0.1 M MES, O.1 M Ammonium sulfate, 5% glycerol, 1.8 mM UDM, pH 6.2, vapor diffusion, hanging drop, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 128.68 α = 90
b = 56.37 β = 96.55
c = 140.19 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD PSI PILATUS 6M -- 2012-07-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 0.9795 APS 24-ID-C

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
1.9 139.27 97.4 0.072 -- -- -- 158163 154051 146309.0 -3.0 --
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)
1.9 1.95 85.6 0.01 -- 1.4 -- --

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 1.9 29.76 -- -- 158163 146309 7722 97.33 -- 0.21606 0.21406 0.25464 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 1.9 1.949 -- 489 9480 0.339 0.379 -- 85.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.0
Anisotropic B[1][1] -1.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 1.92
Anisotropic B[2][2] 0.39
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.1
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.005
r_chiral_restr 0.14
r_dihedral_angle_4_deg 17.151
r_dihedral_angle_3_deg 15.624
r_dihedral_angle_2_deg 34.788
r_dihedral_angle_1_deg 6.301
r_angle_refined_deg 1.508
r_bond_refined_d 0.009
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 13047
Nucleic Acid Atoms 0
Heterogen Atoms 357
Solvent Atoms 937

Software

Computing
Computing Package Purpose
ADSC Data Collection
XDC Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
SOLVE Structure Solution
REFMAC 5.7.0029 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0117 refinement
RESOLVE density modification
SOLVE phasing
Xscale data reduction