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_gen_planes_refined 0.012
r_chiral_restr 0.13
r_dihedral_angle_4_deg 18.914
r_dihedral_angle_3_deg 17.583
r_dihedral_angle_2_deg 32.812
r_dihedral_angle_1_deg 6.542
r_angle_refined_deg 2.09
r_bond_refined_d 0.017
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

Computing
Computing Package Purpose
remdaq Data Collection
INTEGRATE Data Reduction (intensity integration)
XSCALE Data Reduction (data scaling)
Phaser_MR Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.11 data extraction
REFMAC5 version: 5.6.0117 refinement
Xscale data reduction