X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.5
Temperature 298.0
Details PEG 3350, Bis-Tris, NaCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 37.23 α = 90
b = 66.33 β = 90
c = 93.18 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate Osmic mirrors 2009-06-25
Diffraction Radiation
Monochromator Protocol
Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R 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
1.86 25 99.5 0.055 -- -- 5.8 20015 20015 2.0 2.0 13.4
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)
1.86 1.93 95.1 0.151 -- 9.1 5.4 1839

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 1.86 23.85 -- 0.0 -- 19966 1013 99.5 -- 0.195 0.195 0.221 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 1.86 1.98 -- 174 3017 0.212 0.256 0.019 97.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 18.4
Anisotropic B[1][1] 2.15
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.93
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.08
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.5
c_bond_d 0.005
c_scbond_it 2.14
c_mcbond_it 1.21
c_scangle_it 3.21
c_improper_angle_d 0.74
c_mcangle_it 1.7
c_angle_deg 1.4
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.2
Luzzati Sigma A (Observed) 0.07
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.13
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2303
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 166

Software

Software
Software Name Purpose
MAR345dtb data collection
MOLREP phasing
CNS refinement version: 1.1
DENZO data reduction
SCALEPACK data scaling