X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.5
Temperature 289.0
Details 31% PEG 3350, 180 mM LiNO3, 100 mM Sodium Acetate (pH 5.5), 2.5% Hexamine Cobalt Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 50.23 α = 90
b = 50.23 β = 90
c = 103.63 γ = 120
Symmetry
Space Group P 32

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD -- 2010-11-18
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 21-ID-D 1.03318 APS 21-ID-D

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
2.4 -- 99.7 0.04 -- -- 6.4 -- 11411 -- -3.0 65.61
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)
2.4 2.46 100.0 0.614 -- 3.1 6.4 --

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
SAD WITH MR 2.4 43.5 -- 0.0 -- 11384 570 -- -- 0.224 0.222 0.26 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 2.4 2.46 -- 35 777 0.28 0.404 -- 99.15
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 59.79
Anisotropic B[1][1] 11.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 11.15
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -22.3
RMS Deviations
Key Refinement Restraint Deviation
r_dihedral_angle_4_deg 21.769
r_mcangle_it 1.286
r_bond_refined_d 0.01
r_scbond_it 1.61
r_angle_refined_deg 1.922
r_gen_planes_refined 0.005
r_chiral_restr 0.128
r_mcbond_it 0.699
r_scangle_it 2.498
r_dihedral_angle_3_deg 16.021
r_dihedral_angle_2_deg 45.308
r_dihedral_angle_1_deg 4.915
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1130
Nucleic Acid Atoms 729
Heterogen Atoms 2
Solvent Atoms 29

Software

Software
Software Name Purpose
PHASER phasing
REFMAC refinement version: 5.5.0109
XDS data reduction
XSCALE data scaling