8E0R

Crystal structure of mouse APCDD1 in P21 space group


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8E0PPDB entry 8E0P

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72930.7 M magnesium formate, 0.1 M Bis-Tris propane, pH 7.0
Crystal Properties
Matthews coefficientSolvent content
2.1242.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.861α = 90
b = 144.128β = 99.52
c = 64.381γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2019-04-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS-II BEAMLINE 17-ID-20.92009NSLS-II17-ID-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)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
11.94734.36491.10.1350.0570.9968.56.349930
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.9472.121.4640.580.561.3

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 REPLACEMENTTHROUGHOUTPDB entry 8E0P1.953447515240576.640.21110.20920.2471RANDOM9.798
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]
-0.15-0.12-0.010.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.206
r_dihedral_angle_4_deg17.829
r_dihedral_angle_3_deg16.498
r_dihedral_angle_1_deg7.54
r_angle_refined_deg1.405
r_angle_other_deg1.191
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.206
r_dihedral_angle_4_deg17.829
r_dihedral_angle_3_deg16.498
r_dihedral_angle_1_deg7.54
r_angle_refined_deg1.405
r_angle_other_deg1.191
r_chiral_restr0.06
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6656
Nucleic Acid Atoms
Solvent Atoms377
Heterogen Atoms70

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
STARANISOdata scaling