7ZVC

Second crystal form of the mature glutamic-class prolyl-endopeptidase neprosin at 1.85 A resolution.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 7ZU8 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2930.1 M sodium citrate tribasic pH 5.6, 0.5 M ammonium sulphate, 1 M lithium sulphate
Crystal Properties
Matthews coefficientSolvent content
2.5651.89

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 58.86α = 90
b = 40.63β = 107.98
c = 64.63γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2022-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALBA BEAMLINE XALOC0.97926ALBAXALOC

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.8561.597.10.99812.46.5524437
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.851.9160.729

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT7ZU81.8520.662441669097.20.17360.17280.2026RANDOM27.86
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]
-8.30541.40560.72787.5776
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion5.05
t_other_torsion2.39
t_angle_deg1.07
t_bond_d0.011
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
RMS Deviations
KeyRefinement Restraint Deviation
t_omega_torsion5.05
t_other_torsion2.39
t_angle_deg1.07
t_bond_d0.011
t_dihedral_angle_d
t_gen_planes
t_it
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1993
Nucleic Acid Atoms
Solvent Atoms250
Heterogen Atoms91

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
BUSTERrefinement
Cootmodel building