X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.5
Temperature 298.0
Details 100 mM imidazole, pH 6.5, 450 mM sodium acetate, 5 mM tris(2-carboxyethyl)phosphine hydrochloride (TCEP), and 1%(v/v) glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 95.13 α = 90
b = 248.54 β = 106.94
c = 103.46 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV Osmic VariMaxTM HR mirror 2007-12-31
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418 -- --

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
3 40 93.0 0.079 -- -- 2.6 -- 85645 0.0 -2.0 --
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)
3.0 3.11 90.4 43.0 -- 3.8 2.1 8304

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
MIR 3.0 29.89 -- 0.0 -- 83574 4224 91.3 -- 0.257 0.257 0.281 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 3.0 3.19 12492 665 12492 0.429 0.433 0.017 86.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 60.4
Anisotropic B[1][1] 1.83
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 5.22
Anisotropic B[2][2] -0.86
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.96
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.011
c_scbond_it 1.53
c_scangle_it 2.6
c_dihedral_angle_d 23.8
c_improper_angle_d 1.08
c_angle_deg 1.6
c_mcbond_it 1.49
c_mcangle_it 2.72
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.51
Luzzati Sigma A (Observed) 1.08
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.54
Luzzati Sigma A (R-Free Set) 1.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 17092
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 61

Software

Software
Software Name Purpose
CNS refinement version: 1.1
CrystalClear data collection
DENZO data reduction
SCALEPACK data scaling
DM phasing