X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 8.5
Temperature 293.0
Details 0.1M Tris-HCl buffer, 23% PEG3350, 0.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 49.63 α = 77.66
b = 65.37 β = 89.04
c = 69.85 γ = 89.46
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 2013-06-01
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
2.3 50 97.6 -- 0.095 -- -- 38724 38724 -- 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)
2.3 2.34 95.4 -- 0.41 2.41 -- --

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 2.3 49.62 -- 0.0 38724 35341 1874 97.63 -- 0.1892 0.1871 0.2285 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 2.3 2.36 -- 136 2567 0.252 0.265 -- 95.24
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 37.948
Anisotropic B[1][1] 0.43
Anisotropic B[1][2] -0.1
Anisotropic B[1][3] 0.15
Anisotropic B[2][2] -0.81
Anisotropic B[2][3] 0.28
Anisotropic B[3][3] 0.47
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_other 0.005
r_mcangle_it 3.655
r_dihedral_angle_3_deg 20.118
r_mcbond_it 2.231
r_gen_planes_refined 0.008
r_bond_refined_d 0.014
r_mcbond_other 2.23
r_dihedral_angle_2_deg 38.509
r_angle_other_deg 1.135
r_dihedral_angle_1_deg 6.635
r_bond_other_d 0.005
r_angle_refined_deg 1.729
r_dihedral_angle_4_deg 23.167
r_chiral_restr 0.107
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7201
Nucleic Acid Atoms 0
Heterogen Atoms 10
Solvent Atoms 147

Software

Software
Software Name Purpose
MOLREP phasing
REFMAC refinement version: 5.8.0049
HKL-2000 data reduction
HKL-2000 data scaling