5OAU

Penicillin-Binding Protein 2X (PBP2X) from Streptococcus pneumoniae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	290	2.3-3.0 M NaCl, 0.1 M sodium acetate

Crystal Properties
Matthews coefficient	Solvent content
3.57	65.51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 100.26	α = 90
b = 100.26	β = 90
c = 189.81	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	0.97947	ALBA	XALOC

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.67	34.78	99.3	0.1	0.09	7.5	3.5		31872

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.67	2.8	99.1		0.57	0.48	1.7	3.3

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	2.67	34.78	30573	1506	99.88	0.17588	0.17345	0.22531	RANDOM	62.804

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]
-0.05	-0.03		-0.05		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.587
r_dihedral_angle_3_deg	15.943
r_dihedral_angle_4_deg	14.903
r_long_range_B_refined	12.249
r_long_range_B_other	12.247
r_scangle_other	7.953
r_mcangle_it	7.871
r_mcangle_other	7.87
r_dihedral_angle_1_deg	7.28
r_scbond_it	5.464
r_scbond_other	5.464
r_mcbond_it	5.259
r_mcbond_other	5.259
r_angle_refined_deg	1.742
r_angle_other_deg	1.056
r_chiral_restr	0.103
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	5131
Nucleic Acid Atoms
Solvent Atoms	229
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data scaling
XDS	data reduction
MOLREP	phasing