X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 298.0
Details 1X MMT Buffer pH 5.0, 20% PEG1500, vapor diffusion, hanging drop, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.1 α = 90
b = 54.85 β = 90
c = 96.01 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 ADSC QUANTUM 315 -- 2012-06-06
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 24-ID-C 1.0 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
1.8 90 96.6 0.068 -- -- 5.9 -- 23372 -- -- --
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)
1.8 1.86 97.0 0.299 -- -- 5.6 2300

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 1.8 47.63 -- 0.0 -- 23320 1184 96.44 -- 0.1726 0.1709 0.2052 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 1.801 1.848 -- 79 1593 0.261 0.315 -- 94.36
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 31.831
Anisotropic B[1][1] -0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.24
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.16
RMS Deviations
Key Refinement Restraint Deviation
r_angle_refined_deg 1.976
r_dihedral_angle_2_deg 35.103
r_bond_other_d 0.001
r_gen_planes_refined 0.011
r_dihedral_angle_3_deg 14.603
r_dihedral_angle_4_deg 12.591
r_gen_planes_other 0.001
r_angle_other_deg 0.958
r_dihedral_angle_1_deg 6.162
r_bond_refined_d 0.019
r_chiral_restr 0.123
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2237
Nucleic Acid Atoms 0
Heterogen Atoms 48
Solvent Atoms 117

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHASER phasing version: 2.3.0
REFMAC refinement
PDB_EXTRACT data extraction version: 3.11
CrystalClear data collection
DENZO data reduction