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

Software
Software Name Purpose
CNS refinement version: 1.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing