X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.9
Temperature 277.0
Details 15% PEG 8000, 200 MM MG(OAC)2, 100 MM MOPSO, 1MM DTT, 1 MM 1-HYDROXYFARNESYL PHOSPHONATE , pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 126.12 α = 90
b = 126.12 β = 90
c = 119.73 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAC Science DIP-2020 Double focusing Pt/Ni coated mirrors 1999-02-05
Diffraction Radiation
Monochromator Protocol
Pt/Ni coated mirrors SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE MACSCIENCE -- -- --

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
2.7 22.8 98.0 -- 0.102 -- 3.5 -- 26695 -- -2.0 18.7
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)
2.7 2.8 94.7 -- 0.6 1.4 -- 2541

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
FOURIER SYNTHESIS 2.9 50.0 -- -- -- 21638 996 98.6 -- 0.217 0.217 0.244 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 2.9 3.08 -- 160 3434 0.309 0.349 0.028 99.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 46.1
Anisotropic B[1][1] -7.28
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -7.28
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 14.57
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 7.33
c_angle_deg 1.3
c_mcangle_it 5.16
c_scbond_it 5.28
c_improper_angle_d 0.81
c_dihedral_angle_d 19.0
c_mcbond_it 3.33
c_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.35
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.42
Luzzati Sigma A (R-Free Set) 0.54
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4333
Nucleic Acid Atoms 0
Heterogen Atoms 1
Solvent Atoms 0

Software

Computing
Computing Package Purpose
MACSCIENCE Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 0.4 Structure Refinement
Software
Software Name Purpose
SCALEPACK data reduction
CNS version: 0.4 refinement
MACSCIENCE data collection
CNS model building