X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
Temperature 298.0
Details The protein solution containing 10 mg/mL PfDXR, 2 mM inhibitor, 3 mM NADPH, 2 mM MnCl2, 2 mM DTT, 50 mM Tris, pH 7.8 was mixed with an equal volume of the reservoir solution of 0.1 M Tris, pH 8.0, 20% PEG 3350, 0.3 M CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.36 α = 90
b = 77.28 β = 91.5
c = 109.41 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 93
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS HTC Mirrors 2011-08-26
Diffraction Radiation
Monochromator Protocol
MIRROR SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.54178 -- --

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
2.3 51.34 89.2 0.064 -- -- 3.9 -- 34047 -- -- 32.94
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)
2.3 2.42 64.8 0.125 -- 6.9 3.2 3590

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 2.3 44.64 -- 0.0 -- 34035 1698 89.0 -- 0.23 0.23 0.273 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 2.3 2.38 2321 130 2191 0.247 0.32 0.028 61.5
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 37.3
Anisotropic B[1][1] -3.79
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -5.39
Anisotropic B[2][2] -0.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.71
RMS Deviations
Key Refinement Restraint Deviation
c_bond_d 0.007
c_scbond_it 2.12
c_scangle_it 3.05
c_mcbond_it 1.36
c_dihedral_angle_d 21.0
c_improper_angle_d 0.88
c_angle_deg 1.3
c_mcangle_it 2.24
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.24
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6600
Nucleic Acid Atoms 0
Heterogen Atoms 193
Solvent Atoms 138

Software

Software
Software Name Purpose
StructureStudio data collection
PHASER phasing
CNS refinement version: 1.3
MOSFLM data reduction
SCALA data scaling