X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.25
Details 8 MG/ML PROTEIN, 1 MM SACCHAROPINE, 1 MM NADPH, 20 % (W/W) PEG8000, 0.1 M TRIS-HCL PH 7.25, 1 MM DTT

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 86.64 α = 90
b = 205.81 β = 100.05
c = 125.6 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
IMAGE PLATE MARRESEARCH -- 2000-02-15
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE BW7B -- EMBL/DESY, Hamburg BW7B

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
2.1 20 99.7 0.065 -- -- 8.3 -- 250975 -- -3.0 20.6
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 96.5 0.371 -- 2.5 -- --

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 2.1 19.96 -- 0.0 -- 250248 12322 99.6 -- 0.207 0.207 0.228 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 -- 2012 39135 0.257 0.28 0.006 98.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.5
Anisotropic B[1][1] -3.82
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.69
Anisotropic B[2][2] -4.22
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 8.04
RMS Deviations
Key Refinement Restraint Deviation
c_dihedral_angle_d 23.0
c_angle_deg 1.4
c_mcangle_it 1.61
c_scbond_it 1.91
c_improper_angle_d 0.88
c_bond_d 0.007
c_scangle_it 2.71
c_mcbond_it 1.08
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.21
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.25
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 27528
Nucleic Acid Atoms 0
Heterogen Atoms 536
Solvent Atoms 2509

Software

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
EPMR phasing