3LD3 | pdb_00003ld3

Crystal structure of inorganic phosphatase from anaplasma phagocytophilum at 1.75a resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3FQ3	PDB ENTRY 3FQ3 MODIFIED WITH CCP4 PROGRAM CHAINSAW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.2	290	JCSG+ SCREEN CONDITION C6: 100MM PHOSPHATE/CITRATE PH 4.2, 40% PEG 300; ANPHA.01382.A AT 45MG/ ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.38	α = 90
b = 135.38	β = 90
c = 135.38	γ = 90

Symmetry
Space Group	I 21 3

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 315r	Single crystal, cylindrically bent, Si(220)	2009-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.3	0.9765	ALS	5.0.3

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	1.75	20	99.5	0.048	30.24	10.5	41592	41385		-3	30.82

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	1.75	1.8	99.9		0.529	3.7	8.8	3040

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 (All)	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 3FQ3 MODIFIED WITH CCP4 PROGRAM CHAINSAW	1.75	19.96	41592	41385	2062	99.6	0.161	0.161	0.16	0.17	0.182	0.19	RANDOM	12.61

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.905
r_dihedral_angle_4_deg	21.809
r_dihedral_angle_3_deg	12.697
r_dihedral_angle_1_deg	5.646
r_scangle_it	3.793
r_scbond_it	2.322
r_mcangle_it	1.678
r_angle_refined_deg	1.361
r_mcbond_it	0.923
r_angle_other_deg	0.883
r_mcbond_other	0.22
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2597
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	10

Software

Software
Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling