X-RAY DIFFRACTION Experimental Data & Validation

X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.8
Details PROTEIN WAS CRYSTALLIZED FROM 4-6% PEG 3350, 0.2M BIS-TRIS, 0.5M NACL, 5MM H2O2. PH IN THE DROP NEAR 6.8.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 116.61 α = 90
b = 116.61 β = 90
c = 285.61 γ = 120
Symmetry
Space Group H 3 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 287
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR XUONG-HAMLIN MULTIWIRE COLLIMATOR 1996-09
Diffraction Radiation
Monochromator Protocol
GRAPHITE(002) --
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
2.5 58.3 87.6 0.08 0.08 -- 3.9 -- 22669 -- 1.0 34.3
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)
2.5 2.6 39.4 0.188 0.188 3.9 1.5 --

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
MOLECULAR REPLACEMENT 2.55 60.0 -- 2.0 -- 21960 2276 88.6 -- 0.167 0.167 0.23 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 2.55 2.67 -- 156 1241 0.248 0.279 0.04 45.6
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 29.8
Anisotropic B[1][1] 17.434
Anisotropic B[1][2] 7.064
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 17.434
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 17.24
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 1.6
x_mcbond_it 2.76
x_scangle_it 6.195
x_bond_d 0.006
x_improper_angle_d 1.0
x_dihedral_angle_d 23.1
x_mcangle_it 4.242
x_scbond_it 4.297
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.25
Luzzati Sigma A (Observed) 0.28
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.33
Luzzati Sigma A (R-Free Set) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4763
Nucleic Acid Atoms 0
Heterogen Atoms 4
Solvent Atoms 135

Software

Software
Software Name Purpose
UCSD data collection
SCALA data scaling version: IN CCP4
X-PLOR model building version: 3.851
X-PLOR refinement version: 3.851
UCSD data reduction
CCP4 data scaling version: (SCALA)
X-PLOR phasing version: 3.851