2B30 | pdb_00002b30

Initial Crystallographic Structural Analysis of a putative HAD/COF-like hydrolase from Plasmodium vivax

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1L6R	pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM
experimental model	PDB	1NF2	pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM
experimental model	PDB	1NRW	pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM
experimental model	PDB	1RKQ	pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM
experimental model	PDB	1TJ3	pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM
experimental model	PDB	1RLM	pdb entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	PEG 8000, calcium chloride, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.3	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.101	α = 90
b = 101.792	β = 93.93
c = 97.337	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 210		2005-07-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9739	ALS	8.2.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.7	40	99.7	0.102	8.1	3.3	34235	34235		-3	54.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.7	2.85	99.6		0.3	3.2	3.1	4944

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 entries 1L6R, 1NF2, 1NRW, 1RKQ, 1TJ3, and 1RLM	2.7	37.24	32477	32477	1726	99.5	0.20004	0.20004	0.1968	0.21	0.25984	0.22	RANDOM	36.151

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]
0.03		0.03	-0.05		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.606
r_dihedral_angle_4_deg	18.078
r_dihedral_angle_3_deg	15.17
r_dihedral_angle_1_deg	5.932
r_scangle_it	4.052
r_scbond_it	2.7
r_mcangle_it	2.447
r_mcbond_it	1.577
r_angle_refined_deg	1.104
r_angle_other_deg	0.743
r_mcbond_other	0.325
r_symmetry_vdw_other	0.231
r_nbd_refined	0.204
r_metal_ion_refined	0.192
r_nbtor_refined	0.178
r_nbd_other	0.168
r_xyhbond_nbd_refined	0.143
r_symmetry_hbond_refined	0.14
r_symmetry_vdw_refined	0.124
r_nbtor_other	0.081
r_chiral_restr	0.064
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9054
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	8

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing