X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging or Sitting Drop
pH 8
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. Crystals Transferred In Reservoir Solutions Whose Ph Was Increased From 6.0 To 8.0 By Steps Of 0.5 Ph Units (The Soaking Time In Each Solution Was 12 Hours). Manganese Derivative Was Obtained By Soaking For 24 Hours Protein Crystals In The Reservoir Solution Supplemented With 10 Mm MnCl2 (PH 8.00). Crystals Were Frozen In Liquid Propane After Soaking For A Few Seconds In Peg MME 550 (50%), Tris PH 8.0 (40 Mm)., VAPOR DIFFUSION, HANGING OR SITTING-DROP

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 36.12 α = 90
b = 40.76 β = 90
c = 66.02 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 -- 2000-04-16
Diffraction Radiation
Monochromator Protocol
Si111 or Si311 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE BM30A 0.980 ESRF BM30A

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 27 98.2 0.051 -- -- 3.0 -- 6829 -- 0.0 18.2
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)
2.0 2.11 98.2 0.261 -- 2.7 3.1 2970

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 2.0 14.95 -- 0.0 6829 6829 649 84.3 -- -- 0.208 0.246 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 2.0 2.12 -- 103 697 0.238 0.287 0.028 70.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 32.8
Anisotropic B[1][1] 2.74
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -3.74
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.03
c_scbond_it 1.33
c_mcangle_it 1.81
c_mcbond_it 1.1
c_improper_angle_d 0.64
c_bond_d 0.005
c_angle_deg 1.2
c_dihedral_angle_d 23.1
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.26
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 827
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 37

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