1ZJK

Crystal structure of the zymogen catalytic region of human MASP-2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1Q3XSP domain of PDB ENTRY 1Q3X

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8293PEG 6000, sodium chloride, TRIS/HCl buffer, pH 8.0, temperature 293K, VAPOR DIFFUSION, HANGING DROP
Crystal Properties
Matthews coefficientSolvent content
2.243.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.665α = 90
b = 72.689β = 90
c = 110.989γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4toroidal focusing mirror2003-03-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.9392ESRFID14-4

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
12.1828.988.10.09915.138.31833018330-3
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)
12.182.2543.10.5751.91.9800

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)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 REPLACEMENTTHROUGHOUTSP domain of PDB ENTRY 1Q3X2.1828.9173911739193888.180.207330.207330.204910.25285RANDOM25.915
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]
-0.27-2.562.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.19
r_mcangle_it2.135
r_scangle_it1.491
r_mcbond_it1.29
r_scbond_it0.988
r_angle_refined_deg0.875
r_angle_other_deg0.639
r_symmetry_vdw_other0.269
r_nbd_other0.239
r_xyhbond_nbd_refined0.228
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.19
r_mcangle_it2.135
r_scangle_it1.491
r_mcbond_it1.29
r_scbond_it0.988
r_angle_refined_deg0.875
r_angle_other_deg0.639
r_symmetry_vdw_other0.269
r_nbd_other0.239
r_xyhbond_nbd_refined0.228
r_nbd_refined0.201
r_symmetry_vdw_refined0.168
r_symmetry_hbond_refined0.144
r_nbtor_other0.119
r_chiral_restr0.056
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2909
Nucleic Acid Atoms
Solvent Atoms84
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing