5OIZ

Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae in complex with oxacillin

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	277	2.3-3.0 M NaCl, 0.1 M sodium acetate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
3.56	65.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.415	α = 90
b = 100.415	β = 90
c = 189.799	γ = 120

Symmetry
Space Group	P 31 2 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	PIXEL	DECTRIS PILATUS 6M		2015-09-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALBA BEAMLINE XALOC	0.97924	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.7	86.79	99.7	0.137	0.078	0.99	8.5	3.8		30875

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.83	99.9		1.14	0.67	0.58	1.2	3.8

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1K25	2.7	48.54	29554	1601	99.94	0.21985	0.21656	0.28096	RANDOM	63.405

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]
27.61			27.61		-55.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.904
r_dihedral_angle_3_deg	23.502
r_dihedral_angle_4_deg	18.886
r_dihedral_angle_1_deg	8.875
r_long_range_B_refined	5.493
r_long_range_B_other	5.493
r_scangle_other	4.387
r_mcangle_it	3.911
r_mcangle_other	3.91
r_scbond_it	3.368
r_scbond_other	3.365
r_mcbond_other	3.002
r_mcbond_it	3.001
r_angle_refined_deg	2.596
r_angle_other_deg	1.387
r_chiral_restr	0.151
r_bond_refined_d	0.028
r_gen_planes_refined	0.012
r_bond_other_d	0.003
r_gen_planes_other	0.003
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4994
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Coot	model building
SCALA	data scaling
MOLREP	phasing