X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 7.25
Details PROTEIN WAS CRYSTALLIZED FROM 5 % PEG 4000, 100 MM HEPES, PH 7.25, THEN DIRECTLY TRANSFERRED TO 30 % PEG 4000, 50 MM HEPES, PH 7.5, 50 MM NACL. AFTER 12 H, CRYSTALS WERE TRANSFERRED TO 30 % PEG, 75 MM HEPES, PH 7.5, 75 MM NACL, 2.5 MM CACL2, 2.5 MM ATP-GAMMA-S FOR 23 H.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 76.16 α = 90
b = 76.16 β = 90
c = 182.33 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 140
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC MIRRORS 1996-07
Diffraction Radiation
Monochromator Protocol
NI FILTER --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
2.2 20 88.0 0.053 0.053 -- 3.2 -- 28177 -- -3.0 38.2
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)
2.3 2.37 71.7 0.21 0.21 3.2 1.44 --

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 2.3 20.0 -- 0.0 -- 25761 2226 92.1 -- 0.206 0.206 0.269 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 2.3 2.44 -- 245 2830 0.339 0.297 0.019 67.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 53.7
RMS Deviations
Key Refinement Restraint Deviation
x_scangle_it 4.84
x_scbond_it 3.17
x_mcangle_it 4.99
x_mcbond_it 3.1
x_improper_angle_d 1.4
x_bond_d 0.011
x_angle_deg 1.5
x_dihedral_angle_d 24.6
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.32
Luzzati Sigma A (Observed) 0.41
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.38
Luzzati Sigma A (R-Free Set) 0.35
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4634
Nucleic Acid Atoms 0
Heterogen Atoms 64
Solvent Atoms 54

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
X-PLOR 3.851 Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR version: 3.851 model building