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_scangle_it 3.05
c_scbond_it 2.12
c_mcangle_it 2.24
c_mcbond_it 1.36
c_improper_angle_d 0.88
c_dihedral_angle_d 21.0
c_angle_deg 1.3
c_bond_d 0.007
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

Computing
Computing Package Purpose
StructureStudio Data Collection
MOSFLM Data Reduction (intensity integration)
SCALA Data Reduction (data scaling)
Phaser Structure Solution
CNS 1.3 Structure Refinement
Software
Software Name Purpose
CNS version: 1.3 refinement
Phaser model building
StructureStudio data collection