X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.6
Temperature 277.0
Details 1M lithium sulfate, 0.5M ammonium sulfate, pH 5.6, vapor diffusion, hanging drop, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 163.18 α = 90
b = 163.18 β = 90
c = 242.59 γ = 120
Symmetry
Space Group H 3

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- -- 2010-03-08
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.000 Photon Factory BL-17A

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
3 50 96.1 0.057 -- -- 5.6 -- 46293 -- -- --
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)
3.0 3.11 69.2 0.406 -- -- 4.3 3347

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 3.01 50.0 -- 0.0 -- 43230 2202 90.24 -- 0.2505 0.2487 0.2839 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 3.007 3.085 -- 21 501 0.319 0.392 -- 14.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 82.824
Anisotropic B[1][1] -0.01
Anisotropic B[1][2] -0.01
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.01
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.02
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_3_deg 17.616
r_chiral_restr 0.057
r_mcbond_it 0.072
r_dihedral_angle_2_deg 38.634
r_scangle_it 0.416
r_scbond_it 0.24
r_dihedral_angle_4_deg 16.088
r_mcangle_it 0.144
r_gen_planes_refined 0.003
r_dihedral_angle_1_deg 4.1
r_bond_refined_d 0.005
r_angle_refined_deg 0.861
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7546
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 127

Software

Software
Software Name Purpose
SCALEPACK data scaling
PHASER phasing
REFMAC refinement version: 5.5.0102
PDB_EXTRACT data extraction version: 3.10