X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.5
Details PEG 4000, AMONIUM ACETATE, SODIUM HEPES, GLYCEROL, DTT, HMG-COA, pH 7.50

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 75.3 α = 90
b = 130.18 β = 106.48
c = 92.55 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1998-03-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12B -- NSLS X12B

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 38 99.1 0.059 0.059 -- 3.1 -- 101445 -- -3.0 20.1
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)
2.1 2.14 97.5 0.385 0.385 2.5 2.6 --

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
DIRECT 2.1 38.0 -- -- -- 96563 1933 97.0 -- 0.199 0.199 0.239 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 2.1 2.23 -- 318 15986 0.277 0.325 0.018 98.8
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 36.2
Anisotropic B[1][1] -9.86
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 4.28
Anisotropic B[2][2] -4.48
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 14.35
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.9
c_scbond_it 2.03
c_mcangle_it 1.83
c_mcbond_it 1.19
c_improper_angle_d 1.46
c_bond_d 0.011
c_angle_deg 1.5
c_dihedral_angle_d 23.2
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.27
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 12134
Nucleic Acid Atoms 0
Heterogen Atoms 252
Solvent Atoms 281

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHAKE-N-BAKE V. 2.0 Structure Solution
CNS 0.5 Structure Refinement
Software
Software Name Purpose
CNS version: 0.5 refinement
SHAKE-AND-BAKE version: V. 2.0 model building