2ZC5

Penicillin-binding protein 1A (PBP 1A) 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	2ZC6	PDB ENTRY 2ZC6

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.8	293	0.004-0.006M zinc sulfate, 0.05M MES, pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.82	56.38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 185.704	α = 90
b = 50.665	β = 90
c = 110.784	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	CCD	ADSC QUANTUM 315	Rotated-inclined double-crystal monochromator, rhodium-coated horizontal mirror	2007-03-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	1.0000	SPring-8	BL41XU

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	3	29.95	88.1	0.13	6.2	3.9		19127			50.76

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)
	3	3.11	91.5		0.35	2.8	3.6

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 2ZC6	3	29.95	18139	977	88.13	0.2244	0.22158	0.276	RANDOM	50.53

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]
-3.74			0.97		2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.738
r_dihedral_angle_4_deg	19.016
r_dihedral_angle_3_deg	16.506
r_dihedral_angle_1_deg	5.407
r_angle_refined_deg	1.01
r_scangle_it	0.839
r_mcangle_it	0.553
r_scbond_it	0.461
r_mcbond_it	0.305
r_nbtor_refined	0.303
r_symmetry_vdw_refined	0.234
r_nbd_refined	0.197
r_symmetry_metal_ion_refined	0.156
r_xyhbond_nbd_refined	0.135
r_symmetry_hbond_refined	0.125
r_metal_ion_refined	0.114
r_chiral_restr	0.074
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_other
r_symmetry_vdw_other
r_symmetry_hbond_other
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	6300
Nucleic Acid Atoms
Solvent Atoms	6
Heterogen Atoms	56

Software

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