X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion
pH 8
Temperature 293.0
Details 8% PEG4000, 50mM imidazole pH8.0, VAPOR DIFFUSION, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.96 α = 90
b = 140.73 β = 90
c = 144.85 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD RAYONIX MX225HE mirror 2009-12-04
Diffraction Radiation
Monochromator Protocol
Si 111 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.90 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
2.35 41.5 99.3 0.054 0.058 -- 7.3 -- 23814 -- -- --
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)
2.35 2.47 99.8 0.439 0.473 4.4 7.1 --

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 2.35 36.27 -- -- -- 22569 1225 99.15 -- 0.23938 0.23694 0.28231 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 2.347 2.408 -- 88 1650 0.237 0.321 -- 99.31
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 57.619
Anisotropic B[1][1] 3.93
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.74
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.19
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.018
r_dihedral_angle_4_deg 22.256
r_mcangle_it 1.923
r_chiral_restr 0.116
r_dihedral_angle_2_deg 36.45
r_dihedral_angle_1_deg 6.421
r_gen_planes_refined 0.008
r_scangle_it 4.086
r_scbond_it 2.666
r_angle_refined_deg 1.652
r_mcbond_it 1.039
r_dihedral_angle_3_deg 17.29
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2973
Nucleic Acid Atoms 0
Heterogen Atoms 53
Solvent Atoms 65

Software

Software
Software Name Purpose
BSS data collection
MOLREP phasing
REFMAC refinement version: 5.5.0109
HKL-2000 data reduction
HKL-2000 data scaling