3MQD | pdb_00003mqd

Crystal structure of beta-ketoacyl synthase from brucella melitensis with FOL 0758, (1-methyl-1h-indazol-3-yl) methanol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LRF	native structure, 3LRF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5	290	MD PACT SCREEN, H12: 20% PEG 3350, 100MM BISTRISPROPANE PH 8.5, 200MM NA-MALONATE; CRYSTAL SOAKED 100MM MES PH 6.5, 250MM NACL, 30% PEG 3350, 10% GLYCEROL; BRABA.00113.A AT 22.9MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.07	α = 90
b = 83.62	β = 121.37
c = 73.64	γ = 90

Symmetry
Space Group	C 1 2 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 Q315R		2010-04-02		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1		ALS	5.0.1

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	1.25	4181	99.7	0.091	12.07			111226		-3	13.34

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	1.25	1.28	99.1		0.404	4

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	MR	THROUGHOUT	native structure, 3LRF	1.25	41.81	111141	5562	99.8	0.113	0.112	0.12	0.133	0.14	RANDOM	7.42

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]
0.04		0.19	-0.03		0.19

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.148
r_dihedral_angle_4_deg	15.929
r_dihedral_angle_3_deg	11.459
r_dihedral_angle_1_deg	6.464
r_scangle_it	5.373
r_scbond_it	3.772
r_mcangle_it	2.535
r_mcbond_other	2.414
r_mcbond_it	1.777
r_rigid_bond_restr	1.735
r_angle_refined_deg	1.693
r_angle_other_deg	1.315
r_chiral_restr	0.119
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3012
Nucleic Acid Atoms
Solvent Atoms	454
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling