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_mcbond_it 1.787
c_bond_d 0.006
c_scbond_it 2.892
c_angle_deg 1.376
c_improper_angle_d 0.79
c_scangle_it 4.102
c_mcangle_it 2.393
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 5106
Nucleic Acid Atoms 0
Heterogen Atoms 71
Solvent Atoms 463

Software

Software
Software Name Purpose
DENZO data reduction
SCALEPACK data scaling
MLPHARE phasing
CNS refinement