X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 9
Temperature 277.0
Details 2M MgCl2, 0.1M Bicine pH 9.0, 0.1M CoCl2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 183.76 α = 90
b = 183.76 β = 90
c = 183.76 γ = 90
Symmetry
Space Group F 4 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 315r Mirror 1: plane parabola Pt and Rh-coated Invar steel. Mirror 2: torroid Pt and Rh-coated Si --
Diffraction Radiation
Monochromator Protocol
KOHZU: Double crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 8.3.1 1.1159 ALS 8.3.1

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
1.4 50 100.0 -- 0.089 -- 15.0 52653 52634 -- -- --

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 1.4 50.0 -- 0.0 -- 52633 2685 99.98 -- 0.149 0.147 0.174 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 1.4 1.436 -- 195 3631 0.392 0.466 -- 99.97
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 15.513
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 3.897
r_sphericity_free 11.784
r_rigid_bond_restr 2.168
r_scangle_it 6.461
r_scbond_it 4.641
r_mcangle_it 2.74
r_mcbond_other 0.81
r_bond_refined_d 0.024
r_bond_other_d 0.005
r_angle_refined_deg 2.021
r_angle_other_deg 1.692
r_dihedral_angle_1_deg 4.799
r_dihedral_angle_2_deg 37.971
r_dihedral_angle_3_deg 14.385
r_dihedral_angle_4_deg 19.109
r_chiral_restr 0.136
r_gen_planes_refined 0.012
r_gen_planes_other 0.003
r_mcbond_it 1.948
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1418
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 225

Software

Computing
Computing Package Purpose
ADSC Quantum Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.4.0077 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.005 data extraction
REFMAC5 refinement
Phaser molecular replacement