7ZUL | pdb_00007zul

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) in complex with 8Az lactone - Streptococcus pneumoniae R6

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BG1	2BG1 WITHOUT RESIDUES 654 TO 660

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	293	50MM HEPES PH 7.2, 3M NACL, 0.6-0.9M AMMONIUM SULFATE

Crystal Properties
Matthews coefficient	Solvent content
3.33	63.05

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.934	α = 90
b = 149.773	β = 90
c = 98.872	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	PIXEL	DECTRIS PILATUS 2M		2021-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE MASSIF-1	0.965459	ESRF	MASSIF-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	CC (Half)	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	1.744	42.251	97.1	0.1025	0.996	8.01	4.7		71666			38.906

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.744	1.85	91.6		1.972	0.248	0.65	4.4

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2BG1 WITHOUT RESIDUES 654 TO 660	1.744	42.251	71665	2192	97.736	0.181	0.1802	0.19	0.2063	0.22	52.285

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]
-1.993			1.993

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.292
r_dihedral_angle_4_deg	17.911
r_dihedral_angle_3_deg	11.929
r_lrange_it	8.473
r_lrange_other	8.434
r_dihedral_angle_1_deg	7.272
r_scangle_it	5.899
r_scangle_other	5.898
r_scbond_it	4.202
r_scbond_other	4.12
r_mcangle_other	3.117
r_mcangle_it	3.116
r_mcbond_it	2.529
r_mcbond_other	2.524
r_angle_other_deg	1.329
r_angle_refined_deg	1.242
r_symmetry_xyhbond_nbd_refined	0.22
r_nbd_refined	0.203
r_nbd_other	0.194
r_symmetry_nbd_other	0.188
r_nbtor_refined	0.166
r_xyhbond_nbd_refined	0.135
r_symmetry_nbd_refined	0.133
r_xyhbond_nbd_other	0.109
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.06
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_chiral_restr_other	0.001
r_gen_planes_other	0.001
r_bond_other_d

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3506
Nucleic Acid Atoms
Solvent Atoms	383
Heterogen Atoms	55

Software

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