X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Sitting Drop
pH 7.7
Temperature 293.0
Details 0.2M POTASSIUM ACETATE, 20% PEG 3350, pH 7.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 43.92 α = 90
b = 56.57 β = 90
c = 135.84 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MIRRORS 2000-07-20
Diffraction Radiation
Monochromator Protocol
Ni MIRROR + Ni FILTER SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU300 1.5418 -- --

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
2.1 30 92.6 0.064 0.062 -- 4.7 20664 19129 1.0 1.0 8.4
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)
2.1 2.18 90.2 0.139 0.144 11.0 3.6 1813

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 2.1 14.0 -- 0.0 20897 18958 1939 92.9 0.207 0.193 0.193 0.243 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 2.23 -- 286 2711 0.207 0.258 0.015 90.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.1
Anisotropic B[1][1] 4.18
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 1.36
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -5.55
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 2.49
c_scbond_it 1.68
c_mcangle_it 1.67
c_mcbond_it 1.06
c_improper_angle_d 0.85
c_dihedral_angle_d 22.0
c_angle_deg 1.3
c_bond_d 0.006
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.29
Luzzati Sigma A (R-Free Set) 0.18
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2548
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 168

Software

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