X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.5
Temperature 293.0
Details THREE MICROLITERS OF PROTEIN AT A CONCENTRATION OF 6.3MGS/ML IN 10MM TRIS PH 8.0, 200MM NACL, 5% GLYCEROL, LMM DTT, 5MM BME AND 0.1MM EDTA WERE MIXED WITH THREE MICROLITERS OF A RESERVOIR SOLUTION OF 28% PEG400, 100MM SODIUM ACETATE PH 4.5, AND 100MM CADMIUM CHLORIDE AND EQUILIBRATED AGAINST THE SAME., VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.06 α = 90
b = 98.91 β = 105.66
c = 76.86 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MSC/YALE MIRRORS 1999-06-11
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH2R -- -- --

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
1.8 15 97.6 0.053 -- -- 7.0 67929 66308 -- -3.0 25.2
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)
1.8 1.85 95.7 0.237 -- 10.0 7.0 --

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
MIR 1.8 15.0 -- 2.0 67917 66212 4051 97.5 -- 0.182 0.182 0.203 SHELLS
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 1.8 1.85 -- 337 5028 0.207 0.255 -- 95.7
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 22.67
Anisotropic B[1][1] 0.265
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 3.536
Anisotropic B[2][2] -0.776
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.168
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.102
c_scbond_it 2.892
c_mcangle_it 2.393
c_mcbond_it 1.787
c_improper_angle_d 0.79
c_bond_d 0.006
c_angle_deg 1.376
c_dihedral_angle_d 23.88
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.17
Luzzati Sigma A (Observed) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 5096
Nucleic Acid Atoms 0
Heterogen Atoms 71
Solvent Atoms 463

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
MLPHARE Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
MLPHARE model building
SCALEPACK data reduction
DENZO data collection