X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 4.6
Temperature 293.0
Details 0.1 M cadmium chloride hydrate, 0.1 M sodium acetate trihydrate, 30%(v/v) PEG400, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 55.24 α = 90
b = 85.46 β = 90
c = 86.11 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 ADSC QUANTUM 315r -- 2012-12-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98000 Photon Factory BL-17A

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
1.5 50 97.4 -- 0.035 -- 6.3 65724 64012 -- -- --
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)
1.5 1.55 97.4 -- 0.232 3.08 6.3 64012

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 1.5 50.0 -- -- -- 60475 3235 96.94 -- 0.17613 0.1729 0.23616 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 1.502 1.541 -- 252 4332 0.357 0.415 -- 95.74
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.935
Anisotropic B[1][1] -0.4
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.66
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.26
RMS Deviations
Key Refinement Restraint Deviation
r_mcangle_it 3.618
r_rigid_bond_restr 3.63
r_gen_planes_refined 0.009
r_long_range_B_other 5.177
r_angle_other_deg 0.877
r_scbond_it 4.778
r_dihedral_angle_3_deg 14.443
r_mcangle_other 3.619
r_bond_other_d 0.001
r_scangle_other 5.436
r_gen_planes_other 0.002
r_dihedral_angle_2_deg 26.406
r_chiral_restr 0.135
r_bond_refined_d 0.018
r_dihedral_angle_1_deg 7.272
r_sphericity_bonded 10.738
r_mcbond_other 2.952
r_scbond_other 4.779
r_sphericity_free 40.256
r_dihedral_angle_4_deg 12.47
r_angle_refined_deg 1.912
r_mcbond_it 2.999
r_long_range_B_refined 5.176
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3652
Nucleic Acid Atoms 0
Heterogen Atoms 159
Solvent Atoms 233

Software

Software
Software Name Purpose
SERGUI data collection
PHASER phasing
REFMAC refinement version: 5.8.0049
HKL-2000 data reduction
HKL-2000 data scaling