X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Lipidic Mesophase
pH 6.75
Temperature 293.0
Details 30-35% v/v PEG 400, 0.1-0.2 M Na2SO4, 0.1 M Bis-tris propane pH 6.5-7.0, 5-7% 1,4-Butanediol, 8-10% Cholesterol, 52-50% Monoolein, pH 6.75, LIPIDIC MESOPHASE, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 106.32 α = 90
b = 169.24 β = 105.62
c = 40.15 γ = 90
Symmetry
Space Group C 1 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 78
Diffraction Detector
Detector Diffraction Type Details Collection Date
CCD MARMOSAIC 300 mm CCD mirrors 2007-07-18
CCD MARMOSAIC 300 mm CCD mirrors 2007-06-22
Diffraction Radiation
Monochromator Protocol
Double crystal SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON APS BEAMLINE 23-ID-B 1.03321 APS 23-ID-B
SYNCHROTRON APS BEAMLINE 23-ID-B 1.03321 APS 23-ID-B

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
2.4 20 99.2 0.127 -- -- -- 26705 26506 -- -3.0 63.908
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)
2.4 2.5 99.1 0.678 -- 2.2 -- --

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 2.4 19.95 -- 0.0 26506 26506 1310 99.79 0.198 0.198 0.196 0.232 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 2.4 2.461 -- 78 1829 0.27 0.301 -- 98.76
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 63.912
Anisotropic B[1][1] 0.43
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 2.26
Anisotropic B[2][2] -3.46
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 4.25
RMS Deviations
Key Refinement Restraint Deviation
r_scangle_it 5.849
r_scbond_it 4.582
r_mcangle_it 2.767
r_mcbond_other 0.097
r_mcbond_it 2.352
r_symmetry_hbond_refined 0.192
r_symmetry_vdw_other 0.14
r_symmetry_vdw_refined 0.155
r_xyhbond_nbd_refined 0.164
r_nbtor_other 0.107
r_nbtor_refined 0.18
r_nbd_other 0.194
r_bond_refined_d 0.013
r_bond_other_d 0.0
r_angle_refined_deg 1.5
r_angle_other_deg 4.099
r_dihedral_angle_1_deg 3.876
r_dihedral_angle_2_deg 31.604
r_dihedral_angle_3_deg 11.383
r_dihedral_angle_4_deg 12.164
r_chiral_restr 0.06
r_gen_planes_refined 0.001
r_gen_planes_other 0.001
r_nbd_refined 0.187
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3543
Nucleic Acid Atoms 0
Heterogen Atoms 213
Solvent Atoms 48

Software

Computing
Computing Package Purpose
Blu-Ice Data Collection
XDS Data Reduction (intensity integration)
XDS Data Reduction (data scaling)
PHASER Structure Solution
REFMAC 5.2.0019 Structure Refinement
Software
Software Name Purpose
pdb_extract version: 3.000 data extraction
REFMAC5 refinement
Phaser molecular replacement
Xscale data processing