X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 291.15
Details 0.1 M sodium citrate, 25 mM sodium acetate, 24 % (w/v) PEG 4000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 110.99 α = 90
b = 100.14 β = 105.5
c = 86.57 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD Mar225 -- 2009-05-27
Diffraction Radiation
Monochromator Protocol
Bartels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SLS BEAMLINE X06DA 1.0 SLS X06DA

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 19.73 96.1 0.159 -- -- -- -- n/a 3.0 -3.0 24.81
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 2.1 97.4 0.649 -- 2.04 -- --

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 1.9 19.73 -- 0.0 69085 45003 2251 62.69 0.2032 0.2032 0.2007 0.2497 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 -- 76 1432 0.279 0.326 -- 28.81
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.2358
Anisotropic B[1][1] -0.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.42
Anisotropic B[2][2] 0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.13
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 6.542
r_chiral_restr 0.13
r_bond_refined_d 0.017
r_angle_refined_deg 2.09
r_dihedral_angle_4_deg 18.914
r_dihedral_angle_3_deg 17.583
r_dihedral_angle_2_deg 32.812
r_gen_planes_refined 0.012
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4308
Nucleic Acid Atoms 1061
Heterogen Atoms 25
Solvent Atoms 204

Software

Software
Software Name Purpose
XSCALE data scaling
REFMAC refinement version: 5.6.0117
PDB_EXTRACT data extraction version: 3.11
RemDAq data collection
INTEGRATE data reduction
PHASER phasing