X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 6.2
Temperature 293.0
Details PEG 5000MME, ammonium sulfate, sodium cacodylate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 145.61 α = 90
b = 145.61 β = 90
c = 247.53 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS -- 2001-04-27
Diffraction Radiation
Monochromator Protocol
DIAMOND MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL45PX 0.979, 0.9795, 1.02 SPRING-8 BL45PX

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
2.85 50 99.7 -- -- -- -- 63100 62872 0.0 0.0 --
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)
2.85 2.9 99.5 -- -- -- -- --

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
MAD 2.85 50.0 -- 0.0 62776 62321 6303 -- 0.2862 0.2361 0.231 0.297 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 2.85 2.95 5486 593 -- 0.3375 0.4121 -- --
X Ray Diffraction 2.95 3.07 5487 645 -- 0.3051 0.3713 -- --
X Ray Diffraction 3.07 3.21 5492 632 -- 0.2924 0.366 -- --
X Ray Diffraction 3.21 3.38 5580 604 -- 0.2736 0.3419 -- --
X Ray Diffraction 3.38 3.59 5516 645 -- 0.2636 0.3269 -- --
X Ray Diffraction 3.59 3.87 5517 683 -- 0.2546 0.314 -- --
X Ray Diffraction 3.87 4.26 5611 622 -- 0.2268 0.2916 -- --
X Ray Diffraction 4.26 4.87 5648 636 -- 0.1808 0.2493 -- --
X Ray Diffraction 4.87 6.14 5731 616 -- 0.213 0.2839 -- --
X Ray Diffraction 6.14 50.0 5950 627 -- 0.1993 0.2568 -- --
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.78758
c_dihedral_angle_d 22.7978
c_bond_d 0.007728
c_angle_d 1.25246
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.46
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.51
Luzzati Sigma A (R-Free Set) 0.59
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 15950
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 82

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
CNS Structure Refinement
Software
Software Name Purpose
CNS refinement
SHARP model building