3MJC | pdb_00003mjc

Structure of A-type Ketoreductases from Modular Polyketide Synthase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z5L	PDB ENTRY 2Z5L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.75	293	3.1 M ammonium sulfate, 200 mM NaCl, 100 mM sodium cacodylate, pH 6.75, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2		7	293	2.5 M DL-malic acid, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.474	α = 72.79
b = 63.746	β = 67.3
c = 71.551	γ = 89.82

Symmetry
Space Group	P 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	ADSC QUANTUM 315r		2009-06-25	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1		ALS	8.3.1

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	1.48	62.55	95.2	0.066	26.7	2		148637		2	20.3

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)
	1.48	1.51	92.2		0.478	2	2

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 2Z5L	1.48	62.55	62203	148637	7468	95.2	0.215	0.213	0.211	0.243	0.2404	RANDOM	23.36

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]
0.32	0.3	0.19	-0.16	-0.65	0.08

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.73
r_dihedral_angle_4_deg	21.888
r_dihedral_angle_3_deg	15.837
r_dihedral_angle_1_deg	6.027
r_scangle_it	5.677
r_scbond_it	3.853
r_mcangle_it	2.58
r_angle_refined_deg	2.551
r_mcbond_it	1.635
r_chiral_restr	0.186
r_bond_refined_d	0.031
r_gen_planes_refined	0.015
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6852
Nucleic Acid Atoms
Solvent Atoms	512
Heterogen Atoms	6

Software

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