X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.4
Temperature 294.0
Details 300 mM NDSB-195 + 100 mM MES pH 5.4 + 1500 mM Sodium Potassium Tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.51 α = 90
b = 106.51 β = 90
c = 80.66 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2009-10-11
Diffraction Radiation
Monochromator Protocol
Kohzu HLD-4 Double Crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 31-ID 0.97929 APS 31-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
2.5 32.2 100.0 -- -- -- -- 35389 35389 1.0 1.0 --
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)
2.5 2.64 100.0 -- -- -- -- --

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 2.5 30.0 -- -- 35389 33617 1772 99.88 -- 0.16878 0.16737 0.19532 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 2.5 2.565 -- 130 2503 0.223 0.283 -- 99.89
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 35.601
Anisotropic B[1][1] -0.46
Anisotropic B[1][2] -0.23
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.69
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.003
r_chiral_restr 0.08
r_dihedral_angle_4_deg 13.843
r_dihedral_angle_3_deg 15.208
r_dihedral_angle_2_deg 35.99
r_dihedral_angle_1_deg 4.746
r_angle_refined_deg 1.195
r_bond_refined_d 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4238
Nucleic Acid Atoms 0
Heterogen Atoms 126
Solvent Atoms 162

Software

Computing
Computing Package Purpose
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.7.0017 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.7.0017 refinement
PHASER model building