NEUTRON DIFFRACTION - X-RAY DIFFRACTION Experimental Data & Validation


Structure 5CCD has been solved using multiple methods: NEUTRON DIFFRACTION - X-RAY DIFFRACTION

X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7
Temperature 296.0
Details PEG 550 MME, Magnesium Chloride Hexahydrate and HEPES pH 7

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 83.19 α = 90
b = 83.19 β = 90
c = 67.63 γ = 120
Symmetry
Space Group P 32 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
2 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU RAXIS IV++ OSMIC VARIMAX 2014-06-07
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU MICROMAX-007 HF -- -- --
NUCLEAR REACTOR -- -- -- IMAGINE

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 97.1 0.076 -- -- 4.3 -- 13696 -- -- --
2.6 40 74.7 0.196 -- -- 3.5 -- 7175 -- -- --
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)
1.89 2.28 95.2 0.627 -- 2.3 4.4 --

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 -- 3.0 -- 10616 1035 74.7 -- -- 0.203 0.239 RANDOM
MOLECULAR REPLACEMENT 2.6 30.02 -- 3.0 -- 7314 482 76.0 -- -- 0.201 0.214 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)
Neutron Diffraction 2.6 2.72 -- 38 344 0.439 0.516 0.084 33.0
X Ray Diffraction 2.2 2.3 -- 42 380 0.248 0.263 0.041 21.9
RMS Deviations
Key Refinement Restraint Deviation
x_torsion_deg 16.7
x_torsion_impr_deg 0.77
x_bond_d 0.008
x_angle_deg 1.1
x_angle_deg 1.1
x_bond_d 0.008
x_torsion_deg 16.7
x_torsion_impr_deg 0.77
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.51
Luzzati Sigma A (Observed) 1.04
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.69
Luzzati Sigma A (R-Free Set) 1.48
Luzzati ESD (Observed) 0.26
Luzzati Sigma A (Observed) 0.26
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.3
Luzzati Sigma A (R-Free Set) 0.3
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1755
Nucleic Acid Atoms 0
Heterogen Atoms 26
Solvent Atoms 77

Software

Software
Software Name Purpose
CNS refinement version: nCNS 1.0.0
DENZO data processing
SCALEPACK data scaling
HKL-3000 data processing
Coot model building
CNS refinement version: 1.0.0
O model building
PHENIX phasing
nCNS refinement version: 1.0.0