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_sphericity_bonded 2.265
r_sphericity_free 5.518
r_rigid_bond_restr 1.309
r_scangle_it 3.74
r_scbond_it 2.464
r_mcangle_it 1.779
r_mcbond_other 0.413
r_mcbond_it 1.079
r_gen_planes_other 0.001
r_gen_planes_refined 0.007
r_chiral_restr 0.091
r_dihedral_angle_4_deg 11.551
r_dihedral_angle_3_deg 12.403
r_dihedral_angle_2_deg 33.33
r_dihedral_angle_1_deg 6.332
r_angle_other_deg 0.824
r_angle_refined_deg 1.516
r_bond_other_d 0.001
r_bond_refined_d 0.014
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

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.5.0110 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.5.0110 refinement
PHASER model building
HKL-2000 data collection