X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 296.0
Details 2 M ammonium sulfate, 0.1 M HEPES, 0.02% sodium azide , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 74.78 α = 90
b = 82.43 β = 90
c = 123.96 γ = 90
Symmetry
Space Group I 2 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD NONIUS KAPPA CCD2000 OSMIC CONFOCAL MAX-FLUX (GREEN) 2005-01-01
Diffraction Radiation
Monochromator Protocol
OSMIC CONFOCAL MAX-FLUX (GREEN) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE ENRAF-NONIUS FR591 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
1.58 50 98.5 0.048 -- -- 7.7 52683 51888 0.0 -3.0 21.8
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)
1.58 1.64 90.9 0.247 -- 4.4 4.1 4747

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 1.58 20.0 -3.0 0.0 52743 51872 4226 98.3 0.2186 0.2186 0.2172 0.2347 RANDOM, same test set as for pdb ID 2FI3
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 1.58 1.68 7990 678 -- 0.307 0.316 -- 91.9
X Ray Diffraction 1.68 1.81 8624 697 -- 0.253 0.293 -- 99.0
X Ray Diffraction 1.81 1.99 8715 682 -- 0.246 0.281 -- 99.9
X Ray Diffraction 1.99 2.28 8742 714 -- 0.226 0.244 -- 100.0
X Ray Diffraction 2.28 2.87 8834 698 -- 0.213 0.232 -- 99.9
X Ray Diffraction 2.87 20.0 8967 757 -- 0.184 0.193 -- 99.2
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model ISOTROPIC
Mean Isotropic B 16.0
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.165
c_scbond_it 1.516
c_mcangle_it 1.558
c_mcbond_it 1.025
c_improper_angle_d 0.0
c_bond_d 0.005
c_angle_deg 1.34
c_dihedral_angle_d 25.5
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.2
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.22
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2074
Nucleic Acid Atoms 0
Heterogen Atoms 67
Solvent Atoms 240

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement
CNS model building
SCALEPACK data reduction
HKL-2000 data collection