X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.6
Details PROTEIN FROM THE PURPLE MEMBRANE WAS DELIPIDATED AND SOLUBILIZED IN OCTYL GLUCOSIDE. PROTEIN WAS CRYSTALLIZED FROM 60 - 70% (W/W) MONOOLEIN, 0.7 - 4.0 M NA/K - PHOSPHATE IN A PHOSPHATE BUFFER AT PH 5.6, AT 20C AND IN THE DARK. THE MIXTURE WAS CENTRIFUGED AT 10000G FOR 150 MN PRIOR TO CRYSTALLISATION.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 61.76 α = 90
b = 61.76 β = 90
c = 104.16 γ = 120
Symmetry
Space Group P 63

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH ELLIPSOIDAL MIRROR 1996-08
Diffraction Radiation
Monochromator Protocol
SI(111) --
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON ESRF BEAMLINE ID13 -- ESRF ID13

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
2.35 10 91.2 -- 0.1 -- 2.0 -- 8045 -- 0.0 45.5
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)
2.35 2.56 90.4 -- 0.266 2.4 1.6 --

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 2.35 5.0 -- 2.5 -- 6564 300 77.8 -- 0.2582 0.2582 0.317 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 2.35 2.48 -- 49 957 0.3947 0.384 -- 67.0
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 75.0
Anisotropic B[1][1] 0.0
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.0
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.0
RMS Deviations
Key Refinement Restraint Deviation
x_bond_d 0.008
x_angle_deg 1.491
x_improper_angle_d 1.188
x_dihedral_angle_d 20.82
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.4
Luzzati Sigma A (Observed) 0.62
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.51
Luzzati Sigma A (R-Free Set) 0.76
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1694
Nucleic Acid Atoms 0
Heterogen Atoms 20
Solvent Atoms 26

Software

Software
Software Name Purpose
X-PLOR model building version: 3.8
X-PLOR refinement version: 3.8
DENZO data reduction
CCP4 data scaling
X-PLOR phasing version: 3.8