X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 5.3
Temperature 296.0
Details PEG 8000, phosphate-citrate buffer, sodium azide, pH 5.3, VAPOR DIFFUSION, SITTING DROP, temperature 296K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 112.79 α = 90
b = 137.32 β = 95.55
c = 61.87 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 295
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV MIRRORS 1999-08-01
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200H -- -- --

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 40 95.5 0.07 -- -- 3.0 45106 45106 2.0 1.0 29.5
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)
2.2 2.28 90.9 0.331 -- 1.0 2.0 4304

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 2.2 40.0 1.0 2.0 43180 39461 3932 83.2 0.2012 0.185 0.185 0.271 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 2.2 2.34 4452 525 -- 0.2621 0.3118 -- 56.6
X Ray Diffraction 2.34 2.52 5196 563 -- 0.2395 0.2937 -- 66.06
X Ray Diffraction 2.52 2.77 5780 654 -- 0.2278 0.2881 -- 73.01
X Ray Diffraction 2.77 3.17 6374 705 -- 0.2088 0.2769 -- --
X Ray Diffraction 3.17 4.0 6838 752 -- 0.164 0.2653 -- 86.37
X Ray Diffraction 4.0 40.0 6889 733 2051 0.1486 0.2514 -- 86.11
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model isotropic
Mean Isotropic B 35.2
RMS Deviations
Key Refinement Restraint Deviation
x_angle_deg 1.6
x_bond_d 0.008
x_improper_angle_d 1.3
x_dihedral_angle_d 24.3
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Resolution Cutoff (Low) 5.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 6778
Nucleic Acid Atoms 0
Heterogen Atoms 12
Solvent Atoms 421

Software

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