X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 9
Temperature 286.0
Details 0.1 M bicine, pH 9.0, 12-15% PEG400, 25 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 286K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 71.06 α = 90
b = 42.34 β = 98.6
c = 92.59 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 98
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirrors 2009-11-06
Diffraction Radiation
Monochromator Protocol
Rosenbaum-Rock double-crystal Si(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 22-ID 1.0 APS 22-ID

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
1.31 50 97.7 0.107 -- -- 3.7 130862 127861 0.0 0.0 13.1
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)
1.31 1.36 93.6 0.581 -- 2.3 3.4 13007

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 1.31 38.43 -- 0.0 128723 122057 5936 92.9 -- 0.197 0.196 0.209 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 1.31 1.39 -- 868 16579 0.248 0.247 0.008 80.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 19.3
Anisotropic B[1][1] 0.19
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -1.6
Anisotropic B[2][2] 0.19
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.38
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.86
c_scbond_it 1.96
c_mcangle_it 1.7
c_mcbond_it 1.08
c_improper_angle_d 0.63
c_bond_d 0.003
c_angle_deg 0.8
c_dihedral_angle_d 18.8
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.15
Luzzati Sigma A (Observed) 0.11
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.16
Luzzati Sigma A (R-Free Set) 0.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4183
Nucleic Acid Atoms 0
Heterogen Atoms 19
Solvent Atoms 496

Software

Computing
Computing Package Purpose
MAR345dtb Data Collection
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNX Structure Solution
CNX 2005 Structure Refinement
Software
Software Name Purpose
CNX version: 2005 refinement
CNX model building
MAR345dtb data collection