X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5.5
Temperature 277.0
Details MES, ammonium sulfate, PEG 20K, ethylene glycol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 127.55 α = 90
b = 127.55 β = 90
c = 97.6 γ = 120
Symmetry
Space Group P 61

Diffraction

Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- --
CCD MARRESEARCH -- --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
-- MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X4A 0.9792 NSLS X4A
SYNCHROTRON APS BEAMLINE 31-ID 0.9791, 0.9793, 0.9795, 0.9686 APS 31-ID

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
2.8 20 99.7 0.046 -- -- 7.5 22264 22264 -- -- 89.1
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)
2.8 2.9 100.0 0.313 -- -- -- --

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 19.99 -- 0.0 -- 21051 2085 99.6 -- 0.201 0.201 0.273 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 3.03 -- 364 3162 0.316 0.408 0.021 100.0
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 68.2
Anisotropic B[1][1] 2.82
Anisotropic B[1][2] 15.55
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 2.82
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.63
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 11.49
c_scbond_it 8.83
c_mcangle_it 8.48
c_mcbond_it 5.76
c_improper_angle_d 1.07
c_dihedral_angle_d 25.0
c_angle_deg 1.6
c_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.33
Luzzati Sigma A (Observed) 0.37
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.48
Luzzati Sigma A (R-Free Set) 0.53
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3467
Nucleic Acid Atoms 609
Heterogen Atoms 36
Solvent Atoms 46

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
SHARP Structure Solution
CNS 1.1 Structure Refinement
Software
Software Name Purpose
CNS version: 1.1 refinement