7ZUH

PENICILLIN-BINDING PROTEIN 1B (PBP-1B) Streptococcus pneumoniae R6

X-RAY DIFFRACTION

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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
3.32	61.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 95.681	α = 90
b = 147.016	β = 90
c = 98.709	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		2021-06-10	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	1.467	43.06	99.5	0.078	0.998	11.77	5.2		117495			30.38

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	1.467	1.55	99.3		1.973	0.298	0.87	4.9

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	R-Free	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2BG1 WITHOUT RESIDUES 654 TO 660	1.467	43.051	117495	2358	99.107	0.19	0.1894	0.1995	46.129

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]
0.483			-0.109		-0.373

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.903
r_dihedral_angle_4_deg	20.246
r_dihedral_angle_3_deg	13.052
r_lrange_it	9.103
r_lrange_other	8.913
r_dihedral_angle_1_deg	7.757
r_scangle_it	5.462
r_scangle_other	5.461
r_scbond_it	3.757
r_scbond_other	3.756
r_mcangle_it	3.102
r_mcangle_other	3.101
r_mcbond_it	2.473
r_mcbond_other	2.461
r_angle_refined_deg	1.234
r_angle_other_deg	0.988
r_nbd_refined	0.217
r_symmetry_nbd_other	0.191
r_symmetry_xyhbond_nbd_refined	0.186
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.168
r_nbd_other	0.137
r_symmetry_nbd_refined	0.124
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.062
r_gen_planes_refined	0.034
r_gen_planes_other	0.029
r_bond_refined_d	0.009
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3615
Nucleic Acid Atoms
Solvent Atoms	677
Heterogen Atoms	26

Software

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