X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7
Temperature 293.0
Details ammonium sulfate, cadmium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 182.43 α = 90
b = 182.43 β = 90
c = 182.43 γ = 90
Symmetry
Space Group F 4 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE -- 2009-11-26
Diffraction Radiation
Monochromator Protocol
Rotated-inclined double-crystal monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.5080 SPring-8 BL41XU

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 30 100.0 0.094 -- -- 11.3 -- 22730 -- -- 16.771
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 1.92 100.0 0.272 -- -- 11.6 --

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 25.55 -- -- -- 21557 1162 99.93 -- 0.17837 0.1771 0.20283 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 1.852 1.899 -- 99 1554 0.18 0.22 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.087
RMS Deviations
Key Refinement Restraint Deviation
r_scbond_it 2.469
r_gen_planes_refined 0.005
r_mcangle_it 1.412
r_dihedral_angle_3_deg 13.595
r_xyhbond_nbd_refined 0.12
r_symmetry_metal_ion_refined 0.211
r_symmetry_vdw_refined 0.185
r_angle_refined_deg 1.219
r_sphericity_free 16.865
r_dihedral_angle_4_deg 17.119
r_dihedral_angle_1_deg 4.16
r_metal_ion_refined 0.106
r_scangle_it 4.052
r_bond_refined_d 0.011
r_mcbond_it 0.897
r_chiral_restr 0.095
r_dihedral_angle_2_deg 36.389
r_nbd_refined 0.218
r_symmetry_hbond_refined 0.128
r_nbtor_refined 0.304
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1360
Nucleic Acid Atoms 0
Heterogen Atoms 41
Solvent Atoms 153

Software

Software
Software Name Purpose
HKL-2000 data collection
MOLREP phasing
REFMAC refinement version: 5.2.0005
SCALEPACK data scaling