X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7
Details PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION FROM DROPS CONTAINING 4 UL OF PROTEIN SOLUTION (10 MG/ML IN 50 MM TRIS/HCL, PH 8.0) PLUS 4 UL OF RESERVOIR SOLUTION (50 MM HEPES, 1 M AMMONIUM SULFATE, 1% (V/V) PEG 500, PH 7.0) EQUILIBRATED AGAINST 1 ML OF RESERVOIR SOLUTION.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 91.29 α = 90
b = 91.29 β = 90
c = 137.47 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 278
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH BEAM FOCUSSING MIRROR SYSTEM (MSC, USA) 1997-05-15
Diffraction Radiation
Monochromator Protocol
NI FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 -- -- --

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
1.83 25.9 96.9 0.067 -- -- 4.0 -- 55286 -- 0.0 19.7
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)
1.83 1.85 96.1 0.444 -- 2.1 2.6 --

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 1.83 25.89 -- 0.0 -- 53205 1448 93.0 -- 0.147 0.147 0.154 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 1.83 1.94 -- 215 8072 0.228 0.223 0.015 87.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.7
Anisotropic B[1][1] -0.34
Anisotropic B[1][2] 0.23
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.69
RMS Deviations
Key Refinement Restraint Deviation
c_mcangle_it 1.66
c_angle_deg 1.4
c_mcbond_it 1.15
c_bond_d 0.01
c_scbond_it 2.04
c_improper_angle_d 0.84
c_dihedral_angle_d 24.0
c_scangle_it 3.14
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.16
Luzzati Sigma A (Observed) 0.14
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.16
Luzzati Sigma A (R-Free Set) 0.15
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3909
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 324

Software

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