X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 5.2
Details THE CRYSTALLIZATION CONSISTS OF TWO STEPS. FIRST, A MIXTURE OF 5 MG/ML PURPLE MEMBRANE, 0.25% OTG, 1 M AMMONIUM SULFATE, 0.16 M NACL, 0.04 M SODIUM CITRATE (PH5.2) , 0.04% NAN3 WAS INCUBATED AND 15% TREHALOSE AT 305K FOR 5 DAYS. THIS RESULTED IN THE FORMATION OF SPHERICAL VESICLES WITH A DIAMETER OF 50 NM. AFTER SEDIMENTAL MATERIALS WERE REMOVED BY CENTRIFUGATION (4000G X 10 MIN), A SUSPENSION OF THE SPHERICAL VESICLES WAS COOLED TO 278K AND CONCENTRATED BY VAPOR DIFFUSION AGAINST A RESERVOIR SOLUTION CONTAINING 2.0 M AMMONIUM SULFATE 0.08M SODIUM CITRATE (PH 5.2) AND 30% TREHALOSE. INCUBATION FOR A COUPLE OF MONTHS YIELDED HEXAGONAL CRYSTALS.

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 102.4 α = 90
b = 102.4 β = 90
c = 112.3 γ = 120
Symmetry
Space Group P 6 2 2

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE RIGAKU MIRRORS 1998-11-18
Diffraction Radiation
Monochromator Protocol
SI(111) SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON SPRING-8 BEAMLINE BL44B2 -- SPRING-8 BL44B2

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 50 91.7 -- 0.069 -- 14.4 -- 11480 -- 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)
2.5 2.59 55.2 -- 0.304 -- -- --

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 8.0 -- 0.0 -- 11017 561 90.8 -- 0.257 0.257 0.283 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 2.61 -- 41 756 0.371 0.437 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 36.0
Anisotropic B[1][1] -19.7
Anisotropic B[1][2] -9.8
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -19.7
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 13.4
RMS Deviations
Key Refinement Restraint Deviation
x_improper_angle_d 1.22
x_bond_d 0.006
x_angle_deg 1.22
x_dihedral_angle_d 20.1
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1739
Nucleic Acid Atoms 0
Heterogen Atoms 247
Solvent Atoms 18

Software

Computing
Computing Package Purpose
MOSFLM Data Reduction (intensity integration)
CCP4 (SCALA) Data Reduction (data scaling)
X-PLOR Structure Solution
X-PLOR 3.851 Structure Refinement
Software
Software Name Purpose
X-PLOR version: 3.851 refinement
X-PLOR model building