X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 291.0
Details protein solution: 15 mg/ml H4-ldh, 50 mM Na-Hepes pH 7.5, 2.5 mM NADH, 1 mM oxamate. Well solution: 21% PEG 8k, 100 mM Na-HEPES ph 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 59.49 α = 90
b = 161.68 β = 90
c = 137.85 γ = 90
Symmetry
Space Group C 2 2 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1999-10-07
Diffraction Radiation
Monochromator Protocol
platinum mirrors/Ge 111 monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX7.2 1.488 SRS PX7.2

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
2.1 30 96.0 0.05 -- -- 3.31 39237 37680 1.0 1.0 --
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 2.2 91.1 0.114 -- 8.5 3.13 4400

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 20.0 0.0 0.0 37680 35460 1867 95.22 -- 0.17946 0.17676 0.23012 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 2.154 -- 131 2370 0.169 0.231 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.533
Anisotropic B[1][1] 1.05
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.53
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.52
RMS Deviations
Key Refinement Restraint Deviation
p_scangle_it 4.021
p_mcbond_it 0.829
p_bond_d 0.015
p_mcangle_it 1.497
p_scbond_it 2.534
p_xyhbond_nbd 0.148
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5104
Nucleic Acid Atoms 0
Heterogen Atoms 100
Solvent Atoms 318

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing
REFMAC refinement