X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
pH 4.1
Details CRYSTALLISATION WAS PERFORMED BY THE HANGING-DROP VAPOUR DIFFUSION METHOD. EQUAL VOLUMES CATHEPSIN S (CYS25SER) AT 7 MG/ML, INCLUDING THE PEPTIDE ABZ-LEU-THR-BAL-HYP-TYR(NO2)-ASP-NH2 AT 1 MM AND WELL SOLUTION WERE COMBINED AND PLACED OVER A WELL CONTAINING 20% ISOPROPANOL, 20% PEG2000 AND 0.1M SODIUM CITRATE, PH 4.13

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 79.99 α = 90
b = 79.99 β = 90
c = 61.52 γ = 120
Symmetry
Space Group P 31 2 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 120
Diffraction Detector
Detector Diffraction Type Details Collection Date
IMAGE PLATE MARRESEARCH MULTILAYER --
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
ROTATING ANODE RIGAKU RUH3R -- -- --

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
2.2 20 99.4 0.075 -- -- 3.3 -- 11969 -- -- --
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)
2.2 2.24 98.8 0.27 -- 4.5 3.0 --

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 2.2 20.0 -- -- -- 11182 597 99.5 -- 0.196 0.193 0.253 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 2.2 2.26 -- 41 790 0.206 0.336 -- --
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 19.04
Anisotropic B[1][1] 0.04
Anisotropic B[1][2] 0.02
Anisotropic B[1][3] 0.0
Anisotropic B[2][2] 0.04
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] -0.06
RMS Deviations
Key Refinement Restraint Deviation
r_bond_refined_d 0.013
r_mcbond_it 0.739
r_nbd_refined 0.234
r_gen_planes_refined 0.006
r_mcangle_it 1.378
r_angle_other_deg 1.649
r_chiral_restr 0.115
r_symmetry_hbond_refined 0.36
r_xyhbond_nbd_refined 0.154
r_symmetry_vdw_refined 0.234
r_scangle_it 3.712
r_scbond_it 2.289
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 1684
Nucleic Acid Atoms 0
Heterogen Atoms 0
Solvent Atoms 173

Software

Software
Software Name Purpose
REFMAC refinement version: 5.0
DENZO data reduction
SCALEPACK data scaling
AMoRE phasing