X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 293.0
Details 0.1M bicine (pH9.0), 0.1M NaCl, 20% PEG-MME 550, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 142.42 α = 90
b = 118.11 β = 99.87
c = 74.02 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 110
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 210r -- 2012-05-22
Diffraction Radiation
Monochromator Protocol
Fixed-Exit Double Crystal Monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1.00 SPring-8 BL12B2

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 20 98.1 -- -- -- -- 22074 21656 -- -3.0 --
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 3.21 98.4 -- -- -- -- --

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 20.0 -- -- 20809 20576 1072 98.88 -- 0.17694 0.17479 0.21892 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 3.179 -- 68 1292 0.291 0.333 -- 85.86
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 43.224
Anisotropic B[1][1] -4.55
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.91
Anisotropic B[2][2] -7.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 10.42
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_1_deg 7.819
r_scangle_it 1.647
r_chiral_restr 0.095
r_gen_planes_refined 0.008
r_bond_refined_d 0.017
r_dihedral_angle_3_deg 23.182
r_scbond_it 1.004
r_dihedral_angle_4_deg 21.726
r_mcangle_it 1.762
r_dihedral_angle_2_deg 39.156
r_angle_refined_deg 1.376
r_mcbond_it 1.018
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5840
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 95

Software

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