3OLD

Crystal structure of alpha-amylase in complex with acarviostatin I03


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.5
Temperature 293.0
Details 60% 2-methylpentan-2,4 diol, 100mM cacodylate pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 51.99 α = 90
b = 67.76 β = 90
c = 130.47 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
IMAGE PLATE MAR555 FLAT PANEL -- 2009-12-30
Diffraction Radiation
Monochromator Protocol
GRAPHITE SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BSRF BEAMLINE 1W2B 1.0 BSRF 1W2B

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 41.25 99.6 -- -- -- -- 32450 32428 5.0 2.0 13.2
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)
2.0 2.07 96.5 -- -- -- -- --

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 2.0 41.25 -- 0.0 31254 31254 1546 97.9 -- 0.173 0.173 0.194 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 2.0 2.13 -- 248 4667 0.199 0.252 0.016 94.1
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 23.1
Anisotropic B[1][1] 10.53
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -2.47
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -8.06
RMS Deviations
Key Refinement Restraint Deviation
c_improper_angle_d 1.24
c_bond_d 0.006
c_mcangle_it 1.37
c_scbond_it 1.68
c_angle_deg 1.4
c_scangle_it 2.38
c_dihedral_angle_d 24.3
c_mcbond_it 0.96
Coordinate Error
Parameter Value
Luzzati ESD (Observed) 0.19
Luzzati Sigma A (Observed) 0.13
Luzzati Resolution Cutoff (Low) 5.0
Luzzati ESD (R-Free Set) 0.22
Luzzati Sigma A (R-Free Set) 0.19
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 3939
Nucleic Acid Atoms 0
Heterogen Atoms 171
Solvent Atoms 327

Software

Software
Software Name Purpose
MAR345dtb data collection
PHASES phasing
CNS refinement version: 1.2
HKL-2000 data reduction
HKL-2000 data scaling