2W12 | pdb_00002w12

High-resolution crystal structure of the P-I snake venom metalloproteinase BaP1 in complex with a peptidomimetic: insights into inhibitor binding

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1ND1	PDB ENTRY 1ND1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		PEG 2000, TRIS, pH 6.5

Crystal Properties
Matthews coefficient	Solvent content
2.03	40

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38	α = 90
b = 59.5	β = 90
c = 81.8	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	CCD	MARRESEARCH			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1		BESSY	14.1

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	1.46	19.3	98.4	0.06	21.9	7		32970		6.7	8.7

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	1.46	1.55	90.1		0.25	6.7

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 (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	PDB ENTRY 1ND1	1.46	17.77	32627	1631	100	0.149	0.148	0.15	0.178	0.18	RANDOM	10.31

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.447
r_dihedral_angle_4_deg	19.933
r_dihedral_angle_3_deg	11.005
r_dihedral_angle_1_deg	6.255
r_scangle_it	3.999
r_scbond_it	2.662
r_angle_refined_deg	1.861
r_mcangle_it	1.734
r_mcbond_it	1.074
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.224
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.149
r_xyhbond_nbd_refined	0.144
r_chiral_restr	0.134
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1598
Nucleic Acid Atoms
Solvent Atoms	380
Heterogen Atoms	38

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling