2FM6 | pdb_00002fm6

Zinc-beta-lactamase L1 from stenotrophomonas maltophilia (native form)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	280	AS, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 280K

Crystal Properties
Matthews coefficient	Solvent content
2.5	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.07	α = 90
b = 105.07	β = 90
c = 196.04	γ = 120

Symmetry
Space Group	P 65 2 2

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	MARRESEARCH		2005-05-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.979667	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.75	45.5	99.5	0.072	0.072	7.8	7.2	60974	64243	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.85	99.5		0.403	0.403	2	7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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 ENTRY 1SML	1.75	45.5	2	60974	60974	3256	99.5	0.1775	0.1775	0.17616	0.19	0.20301	0.19	RANDOM	17.221

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]
-0.02	-0.01		-0.02		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.56
r_scangle_it	3.597
r_scbond_it	2.231
r_angle_refined_deg	1.453
r_mcangle_it	1.402
r_angle_other_deg	0.823
r_mcbond_it	0.779
r_nbd_refined	0.348
r_symmetry_vdw_other	0.334
r_symmetry_vdw_refined	0.274
r_nbd_other	0.256
r_symmetry_hbond_refined	0.243
r_xyhbond_nbd_refined	0.178
r_metal_ion_refined	0.092
r_chiral_restr	0.086
r_nbtor_other	0.083
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4002
Nucleic Acid Atoms
Solvent Atoms	541
Heterogen Atoms	47

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CCP4	model building
REFMAC	refinement
CCP4	data scaling
CCP4	phasing