X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 291.0
Details Protein stock:10 mg/ml lipovitellin, 0.25 mM sodium citrate; Well: 0.55-0.61 M sodium citrate, 1mM thioglycerol, 1 mM EDTA, 0.05% sodium azide, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 190.17 α = 90
b = 84.52 β = 100.39
c = 89.53 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD CUSTOM-MADE vertically focusing mirror 1998-02-07
Diffraction Radiation
Monochromator Protocol
double crystal Si220 monochromator,double crystal Si111 monochromator SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 1.0332 APS 19-ID

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
1.9 30 74.4 -- 0.064 -- 1.54 82007 82007 0.0 0.0 23.3
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)
1.9 1.99 30.1 -- -- -- -- --

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 1.9 21.6 -- 0.0 81695 81695 983 74.3 0.193 0.193 0.193 0.255 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 1.9 1.99 4076 27 4076 0.299 0.375 0.072 30.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 49.0
Anisotropic B[1][1] -3.11
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.79
Anisotropic B[2][2] 5.26
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -2.16
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 9.0
c_scbond_it 7.04
c_mcangle_it 6.02
c_mcbond_it 4.76
c_improper_angle_d 2.45
c_dihedral_angle_d 25.7
c_angle_deg 2.5
c_bond_d 0.019
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.21
Luzzati Sigma A (Observed) 0.28
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.28
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 8783
Nucleic Acid Atoms 0
Heterogen Atoms 643
Solvent Atoms 1122

Software

Computing
Computing Package Purpose
HKL-2000 Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 0.9,1.0,1.1 Structure Refinement
Software
Software Name Purpose
1.1 refinement
1.0 refinement
CNS version: 0.9 refinement
CNS model building
SCALEPACK data reduction
HKL-2000 data collection