1IWD

Proposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal Structure of a Plant Cysteine Protease Ervatamin B: Insight into the Structural Basis of its Stability and Substrate Specificity.


X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 8.5
Temperature 292.0
Details PEG4000, Tris HCl, Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 48.2 α = 90
b = 58.76 β = 90
c = 69.35 γ = 90
Symmetry
Space Group P 21 21 21

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 293
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH osmic Max-Flux confocal optics 1999-03-09
Diffraction Radiation
Monochromator Protocol
Osmic Max-Flux optic system SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RU200 1.54 -- --

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
1.63 50 99.1 0.048 -- -- 5.6 25294 25048 -3.0 -- 18.1
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)
1.63 1.67 89.2 0.281 -- 4.0 -- --

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 1.63 14.94 -- 0.0 25194 24993 1213 99.2 0.1626 0.161 0.161 0.184 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 1.63 1.73 3952 203 3749 0.256 0.262 0.018 95.7
Temperature Factor Modeling
Temperature Factor Value
Isotropic Thermal Model RESTRAINED
Mean Isotropic B 17.8
Anisotropic B[1][1] 1.72
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] -1.07
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.65
RMS Deviations
Key Refinement Restraint Deviation
c_scangle_it 4.74
c_scbond_it 3.11
c_mcangle_it 1.99
c_mcbond_it 1.31
c_improper_angle_d 0.74
c_dihedral_angle_d 23.8
c_angle_deg 1.2
c_bond_d 0.005
Coordinate Error
Parameter Value
Luzzati ESD (R-Free Set) 0.17
Luzzati Sigma A (R-Free Set) 0.12
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1632
Nucleic Acid Atoms 0
Heterogen Atoms 5
Solvent Atoms 208

Software

Computing
Computing Package Purpose
DENZO Data Reduction (intensity integration)
SCALEPACK Data Reduction (data scaling)
AMORE Structure Solution
CNS 1.0 Structure Refinement
Software
Software Name Purpose
CNS version: 1.0 refinement
AMoRE model building
SCALEPACK data reduction
DENZO data collection