2WV7 | pdb_00002wv7

Intracellular subtilisin precursor from B. clausii

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		0.1M BISTRIS PH 6.5, 0.1M NACL, 1.5M AMMONIUM SULFATE

Crystal Properties
Matthews coefficient	Solvent content
2.12	42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.829	α = 90
b = 119.829	β = 90
c = 106.2	γ = 120

Symmetry
Space Group	P 31

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	ADSC CCD		2009-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.45	46.6	100	0.18	11.6	3.6		62796		1

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	2.45	2.58	99.9		0.66	1.2	3.2

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 1YJC	2.45	46.62	58858	3905	100	0.202	0.197	0.2	0.274	0.27	RANDOM	30.49

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]
2.52	1.26		2.52		-3.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.944
r_dihedral_angle_3_deg	20.752
r_dihedral_angle_4_deg	19.314
r_dihedral_angle_1_deg	6.978
r_angle_refined_deg	1.646
r_scangle_it	1.245
r_scbond_it	0.809
r_mcangle_it	0.435
r_mcbond_it	0.25
r_chiral_restr	0.115
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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	13168
Nucleic Acid Atoms
Solvent Atoms	321
Heterogen Atoms	5

Software

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