X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 22.0
Details IDH, stored in metal-free final buffer, was diluted to 25, 30, 35 and 40 mg/ml using metal-free 2X buffer; (70mM Na2HPO4 , 18 mM citric acid, 200 mM NaCl, 0.4 mM DTT, pH 5.4). and was crystallized from hanging drops using 5 l each of these IDH solutions and 5 l each of 34, 36, 38, 40, 42, and 44 % (NH4)2SO4 solutions in crystallization buffer (35mM Na2HPO4 , 9 mM citric acid, 100 mM NaCl, 0.2 mM DTT at pH 5.4). , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 22K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 103.65 α = 90
b = 103.65 β = 90
c = 149.39 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 1999-01-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ALS BEAMLINE 5.0.2 1.0 ALS 5.0.2

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
1.7 25 92.7 -- -- -- -- 91206 83266 0.0 0.0 17.7
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)
1.7 1.76 84.6 0.212 -- 6.8 -- --

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 1.7 24.79 -- 0.0 74903 83226 8363 92.7 0.185 0.185 0.185 0.211 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 1.7 1.76 -- 725 6723 0.248 0.262 0.01 84.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.4
Anisotropic B[1][1] 2.09
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.09
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -4.17
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.84
c_scbond_it 2.48
c_mcbond_it 1.31
c_angle_deg 1.6
c_improper_angle_d 1.02
c_mcangle_it 2.0
c_bond_d 0.015
c_dihedral_angle_d 25.0
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.16
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.21
Luzzati Sigma A (R-Free Set) 0.14
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3213
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 337

Software

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