2ZJ6 | pdb_00002zj6

Crystal structure of D337A mutant of Pseudomonas sp. MIS38 lipase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z8X	PDB ENTRY 2Z8X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	10% PEG20000, 0.1M MES, 0.2M calcium acetate, 5mM zinc acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.601	α = 90
b = 84.324	β = 96.25
c = 86.901	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	100	CCD	RIGAKU JUPITER 210	mirrors	2007-12-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	2.25	86.39		0.062		5.2	33670	32025

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 2Z8X	2.25	39.69	30382	1627	94.91	0.17081	0.16873	0.18	0.20992	0.22	RANDOM	19.541

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]
1.55		-1.06	-0.61		-1.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.436
r_dihedral_angle_4_deg	18.065
r_dihedral_angle_3_deg	13.572
r_dihedral_angle_1_deg	7.07
r_scangle_it	3.374
r_scbond_it	2.32
r_mcangle_it	1.642
r_angle_refined_deg	1.573
r_mcbond_it	0.97
r_nbtor_refined	0.305
r_nbd_refined	0.207
r_symmetry_vdw_refined	0.205
r_xyhbond_nbd_refined	0.202
r_metal_ion_refined	0.111
r_symmetry_hbond_refined	0.106
r_chiral_restr	0.102
r_symmetry_metal_ion_refined	0.076
r_bond_refined_d	0.018
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4550
Nucleic Acid Atoms
Solvent Atoms	501
Heterogen Atoms	11

Software

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