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, 1.0 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 = 120.34 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 MARRESEARCH -- 1999-02-05
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SSRL BEAMLINE BL7-1 1.08 SSRL BL7-1

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
2.2 49.9 94.0 -- 0.059 -- 4.4 -- 44489 -- -2.0 32.7
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)
2.24 2.28 72.7 -- 0.552 1.7 -- 1676

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 2.25 50.0 -- -- -- 42723 1996 94.6 -- 0.278 0.278 0.296 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 2.25 2.39 -- 261 5103 0.391 0.386 0.024 70.3
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 59.3
Anisotropic B[1][1] -11.71
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -11.71
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 23.42
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.01
c_scbond_it 3.57
c_mcbond_it 2.45
c_angle_deg 2.1
c_dihedral_angle_d 19.6
c_improper_angle_d 1.02
c_mcangle_it 3.78
c_scangle_it 5.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.42
Luzzati Sigma A (Observed) 0.48
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.46
Luzzati Sigma A (R-Free Set) 0.46
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4192
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 51

Software

Software
Software Name Purpose
MAR data collection
SCALEPACK data scaling
CNS refinement
MAR data reduction
CNS phasing