X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.1
Details CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, AND 8.5% PEG 3350. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, AND 17% PEG 3350., vapor diffusion - hanging drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 54.23 α = 90
b = 65.34 β = 90
c = 73.6 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 289
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 1997-08
Diffraction Radiation
Monochromator Protocol
-- --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SRS BEAMLINE PX9.6 -- SRS PX9.6

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 40 95.4 0.054 -- -- 10.6 -- 20244 -- -3.0 19.4
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 2.0 81.5 -- 0.449 4.5 3.6 --

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 1.9 20.0 -- 0.0 -- 20239 981 95.5 -- 0.194 0.194 0.26 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 2.02 -- 151 2788 0.289 0.292 0.024 84.9
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 35.2
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 0.79
x_angle_deg 1.7
x_dihedral_angle_d 30.1
x_mcangle_it 3.21
x_scangle_it 5.44
x_scbond_it 3.41
x_mcbond_it 1.95
x_bond_d 0.008
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.23
Luzzati Sigma A (Observed) 0.25
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.28
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2116
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 89

Software

Software
Software Name Purpose
SHARP phasing
X-PLOR model building version: 3.851
X-PLOR refinement version: 3.851
DENZO data reduction
SCALEPACK data scaling
X-PLOR phasing version: 3.851