X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 6.1
Details PROTEIN WAS CRYSTALLIZED FROM 40% (V/V) ETHANOL WITH 50MM POTASSIUM CACODYLATE, PH 6.1. GROWN IN SITTING DROPS AT 277 K. RESERVOIRS CONTAINED 40% (V/V) ETHANOL, 50MM POTASSIUM CACODYLATE, PH 5.8 - 6.3. PRIOR TO CRYSTALLIZATION, THE PROTEIN WAS DIALYSED AGAINST SODIUM BICARBONATE, PH 8.1, vapor diffusion - sitting drop

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 72.67 α = 90
b = 72.67 β = 90
c = 154.29 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 113
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IIC -- 1996-02
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
1.8 30 94.0 0.082 -- -- 4.8 -- 36895 -- 3.0 24.0

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
MOLECULAR REPLACEMENT 1.8 30.0 -- 0.0 36834 36834 1797 93.8 0.202 0.202 0.197 0.25 RANDOM SELECTION
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model BCORREL (MODIFIED)
RMS Deviations
Key Refinement Restraint Deviation
t_nbd 0.113
t_it 2.83
t_gen_planes 0.013
t_trig_c_planes 0.009
t_incorr_chiral_ct 0.0
t_dihedral_angle_d 19.6
t_angle_deg 1.5
t_bond_d 0.011
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2551
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 268

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
CCP4 (AGROVATA, ROTAVATA) Data Reduction (data scaling)
AMORE Structure Solution
TNT V. 5-E Structure Refinement
Software
Software Name Purpose
TNT version: 5E refinement
AMORE model building
AGROVATA data reduction
ROTAVATA data reduction
DENZO data collection