X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 3.8
Temperature 300.0
Details 100mM sodium acetate buffer, 10mM cupric acetate, 25% ethanol as precipitant, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 29.32 α = 69.25
b = 37.5 β = 79.71
c = 50.74 γ = 85.39
Symmetry
Space Group P 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 298
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH Mirrors 1998-10-29
Diffraction Radiation
Monochromator Protocol
GRAPHITE CRYSTAL SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 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
1.8 20 90.11 0.062 -- -- -- 16633 16633 0.0 0.0 7.8
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 1.9 84.9 -- 0.364 1.73 1.9 2355

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 20.0 0.0 0.0 13549 13549 1356 73.5 -- -- 0.1825 0.2216 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 1.94 893 98 -- 0.2027 0.2452 -- --
X Ray Diffraction 2.03 2.13 1129 138 -- 0.1784 0.218 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model Isotropic
Mean Isotropic B 18.6
Anisotropic B[1][1] -0.02
Anisotropic B[1][2] -0.12
Anisotropic B[1][3] 0.4
Anisotropic B[2][2] 2.27
Anisotropic B[2][3] 1.05
Anisotropic B[3][3] -2.26
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 0.67
c_dihedral_angle_d 23.8
c_angle_deg 1.2
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.24
Luzzati Sigma A (R-Free Set) 0.2
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1642
Nucleic Acid Atoms 0
Heterogen Atoms 2
Solvent Atoms 133

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
MARSCALE Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMoRE model building
MARSCALE data reduction
DENZO data collection