X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LYBHUMAN CATHEPSIN D (PDB ENTRY 1LYB))

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.5LYOPHILIZED PROTEIN DISSOLVED IN WATER TO 12 MG/ML, SITTING DROPS OF PROTEIN SOLUTION AN ALIQUOTA OF PRECIPITANT SOLUTION, COMPOSED OF PEG 4 K 40%, SODIUM CITRATE BUFFER 0.1 M AND AMMONIUM ACETATE 0.2 M, pH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.2646

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.964α = 90
b = 87.186β = 104.43
c = 81.303γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCH1997-04-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.7234.7896.90.06215.911.384399
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.721.7599.30.4132.52.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE RHUMAN CATHEPSIN D (PDB ENTRY 1LYB))1.7234.883681399499.80.2060.2050.256RANDOM
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
Coordinate Error
Structure Solution MethodRefinement High ResolutionRefinement Low Resolution
1849645754.5
RMS Deviations
KeyRefinement Restraint Deviation
s_similar_adp_cmpnt0.069
s_non_zero_chiral_vol0.045
s_similar_dist0.04
s_zero_chiral_vol0.038
s_from_restr_planes0.03
s_angle_d0.025
s_anti_bump_dis_restr0.021
s_bond_d0.007
s_rigid_bond_adp_cmpnt
s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5000
Nucleic Acid Atoms
Solvent Atoms528
Heterogen Atoms229

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement