X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.6
Temperature 298.0
Details 0.07M tris, 0.1M sodium acetate, 12% PEG 4000, 15% glycerol, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.77 α = 90
b = 79.02 β = 90
c = 117.89 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315 -- 2009-11-05
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID -- APS 19-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
1.85 50 99.3 0.072 -- -- 3.7 -- 19903 -- 2.0 --
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)
1.85 1.88 99.6 0.373 -- 4.1 4.1 --

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 1.85 41.5 -- -- -- 18802 1013 99.6 -- 0.154 0.151 0.195 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 1.85 1.9 -- 83 1369 0.172 0.227 -- 99.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.87
Anisotropic B[1][1] 0.16
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.05
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.11
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_2_deg 33.33
r_dihedral_angle_3_deg 12.403
r_mcangle_it 1.779
r_scbond_it 2.464
r_chiral_restr 0.091
r_dihedral_angle_1_deg 6.332
r_gen_planes_other 0.001
r_bond_refined_d 0.014
r_mcbond_other 0.413
r_sphericity_free 5.518
r_gen_planes_refined 0.007
r_bond_other_d 0.001
r_scangle_it 3.74
r_sphericity_bonded 2.265
r_angle_other_deg 0.824
r_mcbond_it 1.079
r_rigid_bond_restr 1.309
r_angle_refined_deg 1.516
r_dihedral_angle_4_deg 11.551
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1738
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 157

Software

Software
Software Name Purpose
HKL-2000 data collection
PHASER phasing
REFMAC refinement version: 5.5.0110
DENZO data reduction
SCALEPACK data scaling