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 = 125.82 α = 90
b = 125.82 β = 90
c = 122.41 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 1999-05-13
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
3 25.5 85.4 -- 0.123 -- 2.3 -- 17178 -- -2.0 9.7
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)
3.0 3.11 76.1 -- 0.471 0.84 -- 1481

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 3.5 50.0 -- -- -- 11109 519 86.7 -- 0.206 0.206 0.247 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 3.5 3.72 -- 73 1835 0.233 0.253 0.03 90.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 31.0
Anisotropic B[1][1] -12.73
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -12.73
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 25.45
RMS Deviations
Key Refinement Restraint Deviation
c_scbond_it 3.15
c_dihedral_angle_d 19.4
c_bond_d 0.008
c_angle_deg 1.4
c_scangle_it 5.29
c_improper_angle_d 0.79
c_mcangle_it 3.83
c_mcbond_it 2.21
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.38
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.37
Luzzati Sigma A (R-Free Set) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4240
Nucleic Acid Atoms 0
Heterogen Atoms 22
Solvent Atoms 52

Software

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