2VID | pdb_00002vid

Serine protease SplB from Staphylococcus aureus at 1.8A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2AS9	PDB ENTRY 2AS9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	SITTING DROP VAPOR DIFFUSION; 20C; GROWN BY MIXING EQUAL VOLUMES OF SPLB (35 MG/ML IN 5MM TRIS-HCL, PH 8.0 CONTAINING 50MM NACL) AND 0.1M TRIS-HCL, PH 8.5-9.0 CONTAINING 30% PEG 3350 (OPTIMIZED HAMPTON RESEARCH INDEX SOLUTION NUMBER 45)

Crystal Properties
Matthews coefficient	Solvent content
2.69	53.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 117.475	α = 90
b = 117.475	β = 90
c = 73.293	γ = 90

Symmetry
Space Group	P 41 21 2

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		2006-08-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6		MPG/DESY, HAMBURG	BW6

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	1.8	20	99	0.06	29.4	14.4		48001		2

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	1.8	1.9	99		0.35	4.2	7.5

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 2AS9	1.8	20	45454	2403	99.8	0.213	0.211	0.21	0.253	0.25	RANDOM	26.62

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]
0.91			0.91		-1.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33
r_dihedral_angle_4_deg	22.105
r_dihedral_angle_3_deg	13.203
r_dihedral_angle_1_deg	6.629
r_scangle_it	3.736
r_scbond_it	2.614
r_mcangle_it	1.804
r_angle_refined_deg	1.516
r_mcbond_it	1.093
r_nbtor_refined	0.313
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.111
r_symmetry_hbond_refined	0.091
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
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	3032
Nucleic Acid Atoms
Solvent Atoms	322
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing