X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 4.6
Temperature 277.0
Details 30% MPD, 0.1 M Na ac, 0.05 M MgCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 38.64 α = 90
b = 72.14 β = 90.12
c = 70.4 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD ADSC QUANTUM 4 -- 2000-07-07
Diffraction Radiation
Monochromator Protocol
Silicon 111 or Silicon 113 SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID14-4 1.004 ESRF ID14-4

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
1.8 50 98.8 0.057 -- -- 3.7 35534 35534 0.0 0.0 16.4
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)
1.8 1.82 97.2 0.7 -- 11.0 3.2 1380

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 1.8 19.86 0.0 0.0 35340 35340 1750 98.4 0.185 0.185 0.185 0.2205 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 1.8 1.91 5778 275 5545 0.196 0.251 0.015 98.4
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 21.7
Anisotropic B[1][1] 0.52
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.06
Anisotropic B[2][2] -1.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 1.4
RMS Deviations
Key Refinement Restraint Deviation
c_angle_deg 1.5
c_dihedral_angle_d 23.2
c_improper_angle_d 1.08
c_scbond_it 2.27
c_mcbond_it 1.31
c_mcangle_it 1.94
c_scangle_it 3.36
c_bond_d 0.01
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.18
Luzzati Sigma A (Observed) 0.07
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.11
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3306
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 270

Software

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