3GOV | pdb_00003gov

Crystal structure of the catalytic region of human MASP-1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ZJK	MASP-1 serine protease domain(unpublished), CCP1 and CCP2 modules of PDB entry 1zjk

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	well 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 coefficient	Solvent content
3.27	62.42

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate	mirrors	2007-11-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X11	0.8148	EMBL/DESY, HAMBURG	X11

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.55	45.98	97.9	0.095	15.96	5.9		19349		-3	30.892

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.55	2.6	97.4		0.472	4.3	5.8	1066

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	MASP-1 serine protease domain(unpublished), CCP1 and CCP2 modules of PDB entry 1zjk	2.55	45.98	19342	989	97.92	0.231	0.231	0.229	0.2463	0.278	0.2912	RANDOM	48.887

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]
0.52			0.19		-0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.278
r_dihedral_angle_4_deg	16.582
r_dihedral_angle_3_deg	13.929
r_dihedral_angle_1_deg	8.419
r_angle_refined_deg	1.163
r_mcangle_it	1.046
r_angle_other_deg	0.824
r_scangle_it	0.674
r_mcbond_it	0.623
r_scbond_it	0.429
r_nbd_refined	0.19
r_nbd_other	0.188
r_nbtor_refined	0.173
r_symmetry_vdw_other	0.157
r_xyhbond_nbd_refined	0.115
r_symmetry_vdw_refined	0.097
r_mcbond_other	0.096
r_symmetry_hbond_refined	0.082
r_nbtor_other	0.081
r_chiral_restr	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3065
Nucleic Acid Atoms
Solvent Atoms	90
Heterogen Atoms	12

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction