X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 298.0
Details Tris, Mono-ammonium dihydrogen phosphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 120.06 α = 90
b = 120.06 β = 90
c = 94.41 γ = 90
Symmetry
Space Group P 43 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV mirrors --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU -- -- --

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
2.01 19.26 -- -- -- -- -- 45400 n/a 0.0 -- 18.8

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
-- 2.1 19.26 -- -- 40746 39043 3893 95.8 -- -- 0.198 0.235 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 2.1 2.2 4603 440 4163 0.268 0.269 0.013 91.9
X Ray Diffraction 2.2 2.31 4679 455 4224 0.249 0.249 0.012 92.7
X Ray Diffraction 2.31 2.46 4821 486 4335 0.223 0.223 0.01 96.2
X Ray Diffraction 2.46 2.64 4920 495 4425 0.208 0.208 0.009 97.7
X Ray Diffraction 2.64 2.91 4967 509 4458 0.213 0.213 0.009 98.0
X Ray Diffraction 2.91 3.33 5015 519 4496 0.213 0.213 0.009 98.3
X Ray Diffraction 3.33 4.19 4865 498 4367 0.182 0.181 0.008 94.6
X Ray Diffraction 4.19 19.26 5173 491 4682 0.192 0.193 0.009 96.3
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 23.92
Anisotropic B[1][1] -0.69
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.69
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.38
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_impr_deg 0.86
x_torsion_deg 22.8
x_angle_deg 1.6
x_bond_d 0.009
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.24
Luzzati Sigma A (Observed) 0.22
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.23
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 4514
Nucleic Acid Atoms 0
Heterogen Atoms 116
Solvent Atoms 385

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
Crystallography & NMR System version: 1.0 refinement