3QH8 | pdb_00003qh8

Crystal structure of a beta-lactamase-like protein bound to AMP from brucella melitensis, long wavelength synchrotron data

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3MD7	PDB entry 3md7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	290	15-18% PEG 3350, 200MM K/NA TARTRATE, 100MM BISTRISPROPANE PH 8.0, BRABA.11339.A.PW27637 AT 18MG/ML SUPPLEMENTED WITH 1MM AMPPNP AND 2MM MGCL2 AT 18MG/ML. CRYO: 21% PEG 3350, 15% EG, 165MM K/NA TARTRATE, 87MM BISTRISPROPANE PH 8.0, 1MM AMPPNP, 2MM MGCL2, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.23	44.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.21	α = 90
b = 75.53	β = 90
c = 98.94	γ = 90

Symmetry
Space Group	C 2 2 21

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		2010-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.3476	ALS	5.0.2

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	1.6	20	99.6	0.069	25.08	12.3	36517	36362		-3	20.91

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	1.6	1.64	95.9		0.39	5.8	6.1	36362

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 (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	MR	THROUGHOUT	PDB entry 3md7	1.6	18.88	36362	36263	1868	99.4	0.145	0.145	0.143	0.15	0.166	0.18	RANDOM	10.64

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]
-0.2			-0.2		0.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.757
r_dihedral_angle_4_deg	16.3
r_dihedral_angle_3_deg	10.998
r_dihedral_angle_1_deg	6.181
r_scangle_it	4.038
r_scbond_it	2.549
r_mcangle_it	1.657
r_angle_refined_deg	1.652
r_angle_other_deg	0.983
r_mcbond_it	0.937
r_mcbond_other	0.286
r_chiral_restr	0.104
r_bond_refined_d	0.015
r_gen_planes_refined	0.008
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2118
Nucleic Acid Atoms
Solvent Atoms	314
Heterogen Atoms	40

Software

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