X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.6
Details PROTEIN WAS CRYSTALLIZED FROM 1.6 M AMMONIUM SULFATE, 0.1M MES, PH 6.0, XTALS WERE RINSED IN CRYOPROTECTANT SOLUTIONS CONSISTING OF RESERVOIR BUFFER WITH AN ADDED 10%, 20% AND 25% GLYCEROL RESPECTIVELY. SELENOMETHIONINE (SEMET)-CONTAINING PROTEIN WAS CRYSTALLIZED UNDER THE SAME CONDITION.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 119.8 α = 90
b = 119.8 β = 90
c = 62.3 γ = 120
Symmetry
Space Group P 61 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 77
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD -- BENT MIRROR 2005-04-03
Diffraction Radiation
Monochromator Protocol
SI 111 MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 14-ID-B -- APS 14-ID-B

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 24.5 99.0 0.07 -- -- 19.3 -- 8544 -- 2.0 118.1
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)
2.8 2.98 98.0 0.95 -- -- 10.0 --

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
MAD 2.8 24.39 -- 0.0 -- 6560 337 95.5 -- 0.25 0.25 0.292 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 2.98 -- 52 926 0.472 0.451 0.063 87.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 80.1
Anisotropic B[1][1] 4.87
Anisotropic B[1][2] 12.88
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 4.87
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -9.73
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.008
c_mcbond_it 2.08
c_dihedral_angle_d 20.0
c_improper_angle_d 1.04
c_scbond_it 4.3
c_angle_deg 1.4
c_scangle_it 6.8
c_mcangle_it 3.68
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.47
Luzzati Sigma A (Observed) 0.6
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.49
Luzzati Sigma A (R-Free Set) 0.61
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1118
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 9

Software

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