X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 9
Details PROTEIN WAS CRYSTALLIZED FROM 3.6 M AMMONIUM SULFATE. CRYSTALS WER SOAKED FOR 1 HOUR IN A THOROUGHLY DEGASSED AND N2 - SATURATED CRYOPROTECTANT SOLUTION MADE BY ADDITION OF 100 MG SUCROSE, 100 MG GLUCOSE AND 8 MG NA-DITHIONATE TO 1 ML OF 70% SATURATED AMMONIUM SULFATE WITH 50 MM TRIS. HCL PH 9.0. THEN THE SOLUTION WAS EXCHANGED AGAINST A CO SATURATED ONE. DISTINCT COLOR CHANGES ACCOMPANIED THE FORMATION OF UNLIGATED MYOGLOBIN FROM MET-MB AND MBCO FROM UNLIGATED MB.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 90.42 α = 90
b = 90.42 β = 90
c = 45.4 γ = 120
Symmetry
Space Group P 6

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 20
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE AREA DETECTOR MARRESEARCH YES 1994-03
Diffraction Radiation
Monochromator Protocol
YES --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X12C -- NSLS X12C

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
1.5 -- 90.0 0.063 0.068 -- 3.0 -- 30947 -- 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)
1.5 1.7 78.0 -- -- -- -- --

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
DIFFERENCE FOURIER 1.5 7.0 -- 0.0 -- 29798 -- 89.0 -- 0.207 0.207 -- --
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 1.5 1.57 -- -- 3348 0.263 -- -- 79.5
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 6.4
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.01
x_angle_deg 1.7
Coordinate Error
Parameter Value
Luzzati Sigma A (Observed) 0.06
Luzzati Resolution Cutoff (Low) 7.0
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1225
Nucleic Acid Atoms 0
Heterogen Atoms 50
Solvent Atoms 118

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK, XSCALE Data Reduction (data scaling)
X-PLOR 3.1 Structure Solution
X-PLOR 3.1 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.1 refinement
X-PLOR version: 3.1 model building