X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Microbatch
pH 7
Temperature 278.0
Details 5-9% Peg 3350, 300 mM NaCl, 1 mM MgATP, 1 mM hydroxycobalamin, pH 7.0, microbatch, temperature 278K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 80 α = 90
b = 80 β = 90
c = 142 γ = 90
Symmetry
Space Group P 41 21 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
2 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH -- 1998-07-01
CCD APS-1 -- 1999-07-01
Diffraction Radiation
Monochromator Protocol
SAGITALLY FOCUSED Si(111) SINGLE WAVELENGTH
SAGITALLY FOCUSED Si(111) MAD
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 19-ID 0.97923, 0.97947, 0.98325, 0.908 APS 19-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
2.05 30 98.1 0.055 -- -- 4.6 29134 29134 0.0 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)
2.05 2.12 97.1 0.281 -- -- 3.9 --

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 + Molecular replacement 2.1 30.0 0.0 0.0 29095 29095 2943 -- 0.206 0.206 0.206 0.288 randomm
RMS Deviations
Key Refinement Restraint Deviation
t_dihedral_angle_d 0.008
t_angle_deg 2.6
t_bond_d 0.015
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2769
Nucleic Acid Atoms 0
Heterogen Atoms 155
Solvent Atoms 292

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE, CNS, DM Structure Solution
TNT Structure Refinement
Software
Software Name Purpose
TNT refinement
DM model building
CNS model building
AMORE model building