3EXM | pdb_00003exm

Crystal structure of the phosphatase SC4828 with the non-hydrolyzable nucleotide GPCP

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CBT	PDB entry 3CBT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.1	295	0.2 M CaCl2, 20% PEG 3350, 1 mM GPCP. Cryoprotected in N-paratone oil, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.941	α = 90
b = 79.706	β = 90
c = 82.507	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	IMAGE PLATE	RIGAKU RAXIS IV	Osmic mirrors	2007-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.54178

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	1.65	50	97.5	0.033	46.02	6.1	29402	29402			24.2

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)
1	1.65	1.71	80.5		0.256	6.29	3.3	2374

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 3CBT	1.65	25.74	27850	1491	97.5	0.17853	0.17741	0.17	0.19911	0.19	RANDOM	24.26

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	34.523
r_dihedral_angle_4_deg	19.245
r_dihedral_angle_3_deg	14.686
r_dihedral_angle_1_deg	5.844
r_scangle_it	3.409
r_scbond_it	2.159
r_angle_refined_deg	1.505
r_mcangle_it	1.351
r_mcbond_it	0.815
r_nbtor_refined	0.306
r_symmetry_vdw_refined	0.254
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.151
r_symmetry_metal_ion_refined	0.147
r_symmetry_hbond_refined	0.114
r_chiral_restr	0.104
r_metal_ion_refined	0.075
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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	1714
Nucleic Acid Atoms
Solvent Atoms	337
Heterogen Atoms	39

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling