4OMB | pdb_00004omb

Phosphate binding protein

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TWY	PDB entry 1TWY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	2.5 M Na Malonate, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.91	35.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 35.444	α = 90
b = 148.092	β = 90
c = 216.452	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	ADSC QUANTUM 315		2011-10-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	0.9508	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.49	122.22	98	0.1466	0.1523	11.89	13.6	183396	186078	2	2	21.08

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	1.49	1.59	91

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1TWY	1.5	122.2	182512	173385	9126	98.34	0.19144	0.19016	0.19	0.21571	0.22	RANDOM	32.52

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]
-1.72			1.16		0.56

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.166
r_dihedral_angle_3_deg	13.867
r_dihedral_angle_4_deg	13.711
r_long_range_B_other	12.307
r_long_range_B_refined	12.27
r_scangle_other	11
r_scbond_other	8.065
r_scbond_it	8.052
r_dihedral_angle_1_deg	5.954
r_mcangle_it	4.455
r_mcangle_other	4.455
r_mcbond_other	3.496
r_mcbond_it	3.495
r_angle_refined_deg	1.639
r_angle_other_deg	1.385
r_chiral_restr	0.089
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_bond_other_d	0.008
r_gen_planes_other	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9024
Nucleic Acid Atoms
Solvent Atoms	447
Heterogen Atoms	24

Software

Software
Software Name	Purpose
EDNA	data collection
BALBES	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling