X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 293.0
Details 0.2M sodium malonate buffer, 18% PEG3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.02 α = 103.49
b = 65.66 β = 89.86
c = 69.82 γ = 90.61
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE mirrors 2013-06-28
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.00000 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
3.1 50 96.7 -- 0.101 -- -- 15888 15888 -- 0.0 --
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)
3.1 3.15 91.8 -- 0.399 2.06 -- --

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 41.89 -- -- 15888 14407 758 96.7 -- 0.19098 0.18816 0.24559 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 -- 58 1049 0.286 0.339 -- 93.34
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 60.137
Anisotropic B[1][1] -2.33
Anisotropic B[1][2] -0.87
Anisotropic B[1][3] -0.32
Anisotropic B[2][2] 3.88
Anisotropic B[2][3] 0.56
Anisotropic B[3][3] -1.62
RMS Deviations
Key Refinement Restraint Deviation
r_long_range_B_other 7.494
r_gen_planes_other 0.003
r_scbond_other 2.68
r_mcangle_it 4.573
r_bond_other_d 0.003
r_mcbond_it 2.703
r_dihedral_angle_2_deg 37.731
r_bond_refined_d 0.01
r_dihedral_angle_4_deg 19.655
r_mcangle_other 4.572
r_long_range_B_refined 7.494
r_scbond_it 2.681
r_dihedral_angle_3_deg 20.6
r_scangle_other 4.582
r_angle_other_deg 0.869
r_dihedral_angle_1_deg 6.682
r_chiral_restr 0.07
r_mcbond_other 2.704
r_angle_refined_deg 1.363
r_gen_planes_refined 0.005
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7218
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 0

Software

Software
Software Name Purpose
MOLREP phasing
REFMAC refinement version: 5.8.0069
HKL-2000 data reduction
HKL-2000 data scaling