X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 5
Temperature 293.0
Details 0.01 M sodium acetate pH 5.0, 0.42 M sodium sulfate, hanging drop, lyngbyastatin 7 dissolved in methanol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 53.4 α = 90
b = 57.42 β = 90
c = 74.33 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
AREA DETECTOR ADSC QUANTUM 210 Rh coated toroidal focusing mirror 2008-06-27
Diffraction Radiation
Monochromator Protocol
Si(111) channel cut SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON NSLS BEAMLINE X6A 0.9537 NSLS X6A

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
1.55 30 99.6 0.044 -- -- 7.7 33573 33573 -- 2.0 20.6
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)
1.55 1.56 84.0 0.55 -- 2.0 4.9 699

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 1.55 28.71 -- -- -- 31822 1696 99.89 -- 0.17754 0.17606 0.2062 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 1.555 1.595 -- 107 2141 0.272 0.33 -- 99.16
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 24.39
Anisotropic B[1][1] 2.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -0.97
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -1.17
RMS Deviations
Key Refinement Restraint Deviation
r_gen_planes_refined 0.008
r_chiral_restr 0.149
r_dihedral_angle_4_deg 20.521
r_dihedral_angle_3_deg 12.535
r_dihedral_angle_2_deg 36.827
r_dihedral_angle_1_deg 6.402
r_angle_refined_deg 1.709
r_bond_refined_d 0.013
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1890
Nucleic Acid Atoms 0
Heterogen Atoms 6
Solvent Atoms 243

Software

Computing
Computing Package Purpose
DCS_X6A Data Collection
HKL-2000 Data Reduction (intensity integration)
HKL-2000 Data Reduction (data scaling)
MOLREP Structure Solution
REFMAC 5.6.0117 Structure Refinement
Software
Software Name Purpose
REFMAC version: 5.6.0117 refinement
MOLREP model building
DCS_X6A data collection