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, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 183.89 α = 90
b = 183.89 β = 90
c = 183.89 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 0.088 0.088 -- 13.6 -- 52741 -- -- --
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)
1.4 1.48 100.0 0.969 0.969 0.8 13.7 7566

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 -- 52741 2689 99.99 -- 0.137 0.136 0.159 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 -- 210 3605 0.398 0.438 -- 100.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 16.983
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_bonded 4.74
r_sphericity_free 15.282
r_rigid_bond_restr 2.7
r_scangle_it 7.613
r_scbond_it 5.375
r_mcangle_it 3.026
r_mcbond_other 0.964
r_bond_refined_d 0.028
r_bond_other_d 0.001
r_angle_refined_deg 2.141
r_angle_other_deg 1.724
r_dihedral_angle_1_deg 4.754
r_dihedral_angle_2_deg 38.192
r_dihedral_angle_3_deg 14.292
r_dihedral_angle_4_deg 15.94
r_chiral_restr 0.137
r_gen_planes_refined 0.013
r_gen_planes_other 0.003
r_mcbond_it 2.243
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1429
Nucleic Acid Atoms 0
Heterogen Atoms 17
Solvent Atoms 292

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 version: 5.4.0077 refinement
SCALA version: 3.2.5 data processing
Mosflm reflection data processing