X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6
Temperature 293.0
Details PEG 4000, sodium acetate, sodium formate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.33 α = 90
b = 92.39 β = 90
c = 252.76 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX300HE -- 2015-04-12
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90000 SPring-8 BL44XU

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
3.1 50 97.2 -- -- -- 4.5 -- 36834 -- -- --

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 3.1 50.0 -- -- -- 34702 1807 97.17 -- 0.27051 0.26861 0.30744 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 3.1 3.18 -- 135 2467 0.422 0.452 -- 95.56
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 113.175
Anisotropic B[1][1] 10.78
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -5.69
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.09
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_other 4.508
r_dihedral_angle_4_deg 16.218
r_angle_refined_deg 1.124
r_scbond_other 1.411
r_scangle_other 2.534
r_chiral_restr 0.057
r_mcbond_other 1.521
r_bond_refined_d 0.007
r_gen_planes_refined 0.004
r_mcangle_other 2.654
r_long_range_B_refined 4.508
r_mcangle_it 2.654
r_angle_other_deg 0.908
r_dihedral_angle_2_deg 32.074
r_mcbond_it 1.522
r_scbond_it 1.411
r_bond_other_d 0.002
r_dihedral_angle_1_deg 5.479
r_gen_planes_other 0.001
r_dihedral_angle_3_deg 17.867
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 10096
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
REFMAC refinement version: 5.8.0131
HKL-2000 data reduction
HKL-2000 data scaling
MOLREP phasing