4MLL | pdb_00004mll

The 1.4 A structure of the class D beta-lactamase OXA-1 K70D complexed with oxacillin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1M6K	PDB ENTRY 1M6K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	298	10% (w/v) PEG 6000, 0.1 M NaCl, 0.05 M MES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.919	α = 80.9
b = 72.609	β = 69.87
c = 73.446	γ = 71.44

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	MARMOSAIC 300 mm CCD		2012-03-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-D	1.1	APS	21-ID-D

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	1.37	50	94.9	0.065	9.5	3.4		187539

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	1.37	1.42	91.6		0.421	3.2	3.1

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 1M6K	1.37	33.23	187539	178142	9375	94.75	0.16476	0.16316	0.17	0.19581	0.2	RANDOM	21.186

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]
0.73	-0.01	0.28	0.86	0.07	-1.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.055
r_dihedral_angle_4_deg	20.249
r_dihedral_angle_3_deg	13.903
r_dihedral_angle_1_deg	6.705
r_scbond_it	3.474
r_mcangle_it	2.821
r_mcbond_it	2.071
r_mcbond_other	2.07
r_angle_refined_deg	1.66
r_angle_other_deg	0.838
r_chiral_restr	0.104
r_gen_planes_refined	0.014
r_bond_refined_d	0.012
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7884
Nucleic Acid Atoms
Solvent Atoms	945
Heterogen Atoms	171

Software

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