1U2H | pdb_00001u2h

X-ray Structure of the N-terminally truncated human APEP-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1FHGSWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6)
experimental modelPDB 1BIHSWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6)
experimental modelPDB 1CS6SWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP4.629330% PEG MME 2000, 200mM (NH4)2SO4, 100mM Na Acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
1.832.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.541α = 90
b = 25.522β = 104.59
c = 42.544γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHmirrors2004-02-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.20.9184BESSY14.2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
10.962089.10.070.0729.93.918313046733
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
0.960.9847.30.160.164.51.91651

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTSWISS MODEL (PDB ENTRIES 1FHG, 1BIH, 1CS6)0.96543956238489.670.161130.160530.180.172130.19RANDOM7.249
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]
-0.64-0.380.58-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.676
r_dihedral_angle_3_deg13.534
r_dihedral_angle_4_deg9.418
r_sphericity_free8.013
r_dihedral_angle_1_deg6.654
r_scangle_it3.808
r_sphericity_bonded3.157
r_angle_other_deg3
r_scbond_it2.94
r_mcangle_it2.387
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.676
r_dihedral_angle_3_deg13.534
r_dihedral_angle_4_deg9.418
r_sphericity_free8.013
r_dihedral_angle_1_deg6.654
r_scangle_it3.808
r_sphericity_bonded3.157
r_angle_other_deg3
r_scbond_it2.94
r_mcangle_it2.387
r_mcbond_it1.917
r_angle_refined_deg1.782
r_rigid_bond_restr1.302
r_mcbond_other0.671
r_symmetry_vdw_other0.323
r_symmetry_vdw_refined0.289
r_nbd_refined0.217
r_nbd_other0.217
r_symmetry_hbond_refined0.211
r_xyhbond_nbd_refined0.185
r_nbtor_refined0.174
r_chiral_restr0.099
r_nbtor_other0.088
r_bond_refined_d0.015
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms766
Nucleic Acid Atoms
Solvent Atoms150
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing