3DKX | pdb_00003dkx

Crystal Structure of the replication initiator protein encoded on plasmid pMV158 (RepB), trigonal form, to 2.7 Ang resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	298	10% PEG 8000, 100 mM CaCl2, 50mM TRIS HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.611	α = 90
b = 85.611	β = 90
c = 245.53	γ = 120

Symmetry
Space Group	P 32 2 1

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 QUANTUM 210		2004-04-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210		2003-04-14	M	SAD
3	1	x-ray	100	CCD	ADSC QUANTUM 210		2003-07-12	M	MAD
4	1	x-ray	100	CCD	ADSC QUANTUM 210		2006-02-23	M	MAD
5	1	x-ray	100	IMAGE PLATE	MAR scanner 345 mm plate		2006-02-14	M	SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.0052	ESRF	ID29
2	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97920	ESRF	ID14-4
3	SYNCHROTRON	ESRF BEAMLINE BM14	0.9791, 0.9686	ESRF	BM14
4	SYNCHROTRON	ESRF BEAMLINE ID29	1.07207, 1.07244, 1.06736	ESRF	ID29
5	ROTATING ANODE	RIGAKU	1.54179

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
1,2,3,4,5	2.7	24.95	99.9	0.1	15.1	6.5	29602	29572		-3	71.2

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)
	2.7	2.85	100		0.748	2.4	6.7	4243

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	MAD	THROUGHOUT	2.7	24.95	29518	28019	1499	100	0.23048	0.22814	0.23	0.27574	0.27	RANDOM	46.33

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]
1.46	0.73		1.46		-2.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.31
r_dihedral_angle_4_deg	25.398
r_dihedral_angle_3_deg	21.255
r_dihedral_angle_1_deg	5.387
r_scangle_it	2.081
r_angle_refined_deg	1.478
r_scbond_it	1.229
r_mcangle_it	0.975
r_mcbond_it	0.513
r_chiral_restr	0.091
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4928
Nucleic Acid Atoms
Solvent Atoms	122
Heterogen Atoms	7

Software

Software
Software Name	Purpose
REFMAC	refinement
ProDC	data collection
MOSFLM	data reduction
SCALA	data scaling
SHELX	phasing
DM	phasing
DMMulti	phasing