2ZC3

Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2Z2L	PDB ENTRY 2Z2L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	10-25% PEG4000, 0.2M ammonium sulfate, 0.1M sodium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 106.789	α = 90
b = 171.909	β = 90
c = 88.666	γ = 90

Symmetry
Space Group	P 21 21 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS V	A fixed exit SI double crystal monochromator followed bystandard double crystal monochromator and RH-coated downward-deflection mirror with a typical glancing angle of 3.7MRAD	2006-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32B2	1.0000	SPring-8	BL32B2

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	2.5	29.51	92.7	0.059	18.9	5.3		53714			52.76

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)
	2.5	2.58	90.1		0.228	5.5	4.8

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	PDB ENTRY 2Z2L	2.5	29.51	50660	2691	93.26	0.2369	0.23452	0.28126	RANDOM	47.99

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]
2.86			-3.53		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.593
r_dihedral_angle_3_deg	14.657
r_dihedral_angle_4_deg	14.089
r_dihedral_angle_1_deg	5.257
r_scangle_it	1.037
r_angle_refined_deg	0.96
r_mcangle_it	0.662
r_scbond_it	0.602
r_mcbond_it	0.37
r_nbtor_refined	0.293
r_nbd_refined	0.18
r_symmetry_vdw_refined	0.131
r_xyhbond_nbd_refined	0.126
r_symmetry_hbond_refined	0.083
r_chiral_restr	0.065
r_bond_refined_d	0.007
r_gen_planes_refined	0.002
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9881
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	53

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
CrystalClear	data reduction
CrystalClear	data scaling