X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 293.0
Details 5 mg/ml protein; 100 mM TRIS/HCl; 8% (w/v) PEG(6000), pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.48 α = 90
b = 121.28 β = 93.18
c = 89.96 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ENRAF-NONIUS FAST -- 1995-08-01
Diffraction Radiation
Monochromator Protocol
Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU 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
2.8 10 94.4 0.107 -- -- 3.8 105939 100006 0.0 5.0 72.0
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)
2.8 2.95 82.1 -- -- 3.2 -- --

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 2.8 20.0 0.0 0.0 25349 25349 2509 95.1 0.181 0.181 0.181 0.212 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 2.8 2.97 -- 264 2395 0.28 0.31 0.019 57.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 34.3
Anisotropic B[1][1] -2.48
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 7.56
Anisotropic B[2][2] 6.6
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.12
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 26.6
c_angle_deg 1.6
c_scangle_it 6.99
c_mcangle_it 5.1
c_bond_d 0.008
c_improper_angle_d 0.85
c_mcbond_it 3.23
c_scbond_it 5.15
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.29
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.34
Luzzati Sigma A (R-Free Set) 0.51
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 7112
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 16

Software

Software
Software Name Purpose
AMoRE phasing
CNS refinement version: 1.0
MADNES data reduction