4Q8R

Crystal structure of a Phosphate Binding Protein (PBP-1) from Clostridium perfringens

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.5	298	60 mg/mL protein, 0.1 N sodium acetate, pH 4.5, 0.2 M zinc acetate, 10% PEG3000, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 70.78	α = 90
b = 105.73	β = 90
c = 146.45	γ = 90

Symmetry
Space Group	F 2 2 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	PIXEL	DECTRIS PILATUS 6M		2012-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.8000	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.65	37.564	99.9			33131	33131	3	3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.65	1.75	100

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 4GD5	1.65	37.564	31475	1657	99.9	0.13474	0.13239	0.17843	RANDOM	33.254

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]
0.6			-1.3		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_sphericity_free	42.001
r_dihedral_angle_2_deg	35.826
r_sphericity_bonded	20.836
r_dihedral_angle_3_deg	13.665
r_dihedral_angle_4_deg	12.46
r_rigid_bond_restr	8.864
r_long_range_B_refined	6.227
r_scangle_other	5.951
r_dihedral_angle_1_deg	5.861
r_long_range_B_other	5.549
r_scbond_other	5.322
r_scbond_it	5.313
r_mcangle_other	3.782
r_mcangle_it	3.778
r_mcbond_other	3.287
r_mcbond_it	3.27
r_angle_other_deg	2.903
r_angle_refined_deg	1.944
r_chiral_restr	0.135
r_bond_refined_d	0.02
r_gen_planes_other	0.013
r_gen_planes_refined	0.008
r_bond_other_d
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_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1818
Nucleic Acid Atoms
Solvent Atoms	196
Heterogen Atoms	9

Software

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