X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging or Sitting Drop
pH 6
Temperature 285.0
Details MES 50mM PH6.0, PEG MME 550 32% AT 285K. The Protein Was Concentrated at 2 MG/ML In MES-NAOH PH 6.00 (20 mM), DTT (5 mM) And Mixed With An Equal Volume Of The Reservoir Solution Containing PEG MME 550 (32%), MES PH 6.00 (40 mM), DTT (5 mM). Crystal Size (300X40X40 microM3) In 20microL Sitting Drops. Manganese Derivative Was Obtained By Soaking For 24 Hours. Protein Crystals In The Reservoir Solution Were Supplemented With 20 Mm MnCl2 (PH 6.00).Crystals Were Frozen In Liquid Propane After Soaking For A Few Seconds In PEG MME 550 (50%), MES PH 6.00 (40 mM)., VAPOR DIFFUSION, HANGING OR SITTING-DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.84 α = 90
b = 41.02 β = 90
c = 67.01 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAR scanner 345 mm plate -- 1999-06-25
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON LURE BEAMLINE DW32 0.963 LURE DW32

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
1.6 26 97.1 0.04 -- -- 3.3 -- 13445 -- 0.0 20.0
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)
1.6 1.69 94.8 0.178 -- 3.9 3.1 5740

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
FOURIER SYNTHESIS 1.6 20.0 -- 0.0 13445 13445 1339 92.8 -- -- 0.208 0.223 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 1.6 1.7 -- 187 1800 0.225 0.26 0.019 86.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 20.1
Anisotropic B[1][1] -0.08
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.34
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.41
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.41
c_scbond_it 1.67
c_mcangle_it 1.65
c_mcbond_it 1.07
c_improper_angle_d 0.65
c_dihedral_angle_d 22.3
c_angle_deg 1.2
c_bond_d 0.004
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.2
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 899
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 83

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
CNS Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
CNS model building
SCALA data reduction
MOSFLM data collection