X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 6.3
Details THE UNLIGANDED MN12H2 FAB WAS CRYSTALLIZED FROM 20% V/V MPD, 50 MM MES BUFFER, PH 6.3, 20 MM CDCL2.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 114.62 α = 90
b = 85.86 β = 122.69
c = 87.13 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MAC Science DIP-2020 COLLIMATOR 1998-03-01
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
-- ENRAF-NONIUS FR571 -- -- --

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
2.5 20 99.7 0.095 0.095 -- 7.2 -- 15404 -- 0.0 --
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)
2.29 2.5 99.0 0.32 0.32 3.8 3.4 --

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 2.5 20.0 -- 0.0 -- 24596 2417 99.7 -- -- 0.231 0.27 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 2.5 2.59 -- 253 2131 0.316 0.364 -- --
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 27.3
Anisotropic B[1][1] -0.59
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] -3.07
Anisotropic B[2][2] -4.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.639
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 3.58
c_scbond_it 3.58
c_mcangle_it 3.2
c_mcbond_it 3.2
c_improper_angle_d 0.787
c_bond_d 0.008
c_angle_deg 1.624
c_dihedral_angle_d 26.34
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.38
Luzzati Sigma A (Observed) 0.17
Luzzati ESD (R-Free Set) 0.45
Luzzati Sigma A (R-Free Set) 0.34
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3387
Nucleic Acid Atoms 0
Heterogen Atoms 3
Solvent Atoms 173

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
CNS Structure Solution
CNS 3.63 Structure Refinement
Software
Software Name Purpose
CNS version: 3.63 refinement
CNS model building
SCALEPACK data reduction
DENZO data collection