3GOV

Crystal structure of the catalytic region of human MASP-1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ZJKMASP-1 serine protease domain(unpublished), CCP1 and CCP2 modules of PDB entry 1zjk

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.5298well solution: 11%(w/v) PEG3350, 0.1 M MES; protein solution: 50 mM NaCl, 5 mM Tris, 0.5 mM EDTA, 20 mM benzamidine-HCl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.2762.42

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.418α = 90
b = 70.412β = 90
c = 121.413γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm platemirrors2007-11-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X110.8148EMBL/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
12.5545.9897.90.09515.965.919349-330.892
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)
12.552.697.40.4724.35.81066

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTMASP-1 serine protease domain(unpublished), CCP1 and CCP2 modules of PDB entry 1zjk2.5545.981934298997.920.2310.2310.2290.278RANDOM48.887
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]
0.520.19-0.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.278
r_dihedral_angle_4_deg16.582
r_dihedral_angle_3_deg13.929
r_dihedral_angle_1_deg8.419
r_angle_refined_deg1.163
r_mcangle_it1.046
r_angle_other_deg0.824
r_scangle_it0.674
r_mcbond_it0.623
r_scbond_it0.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.278
r_dihedral_angle_4_deg16.582
r_dihedral_angle_3_deg13.929
r_dihedral_angle_1_deg8.419
r_angle_refined_deg1.163
r_mcangle_it1.046
r_angle_other_deg0.824
r_scangle_it0.674
r_mcbond_it0.623
r_scbond_it0.429
r_nbd_refined0.19
r_nbd_other0.188
r_nbtor_refined0.173
r_symmetry_vdw_other0.157
r_xyhbond_nbd_refined0.115
r_symmetry_vdw_refined0.097
r_mcbond_other0.096
r_symmetry_hbond_refined0.082
r_nbtor_other0.081
r_chiral_restr0.071
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3065
Nucleic Acid Atoms
Solvent Atoms90
Heterogen Atoms12

Software

Software
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
XDSdata reduction