Experiment: 1TVF

Crystal Structure of penicillin-binding protein 4 (PBP4) from Staphylococcus aureus

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1HD8	Arp/Warp autobuilt model using phases from two Ta6Br12 clusters and a poor molecular replacement solution. MR was carried out using a model derived from PDB entry 1HD8, which is a mutant of PBP5, sharing ~26% identity with PBP4 over a 245 residue range. Phase combination with MR solution was necessary, as Ta6Br12 clusters occupied positions on the symmetry planes resulting in centrosymmetric phases and hence uninterpretable maps.

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.6	291	24% PEG 4000, 100mM citrate buffer, 200mM Ammonium Sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.58	51.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 48.713	α = 90
b = 140.189	β = 90
c = 145.775	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	MARRESEARCH		2001-10-23	M	SINGLE WAVELENGTH
2	1	x-ray	100	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9A	0.98	NSLS	X9A
2	SYNCHROTRON	NSLS BEAMLINE X9A	1.25	NSLS	X9A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2	30	98.9	0.058	17.1	3.5	67865	67865			9.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.07	98.7		0.196	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SIRAS, MOLECULAR REPLACEMENT	THROUGHOUT	Arp/Warp autobuilt model using phases from two Ta6Br12 clusters and a poor molecular replacement solution. MR was carried out using a model derived from PDB entry 1HD8, which is a mutant of PBP5, sharing ~26% identity with PBP4 over a 245 residue range. Phase combination with MR solution was necessary, as Ta6Br12 clusters occupied positions on the symmetry planes resulting in centrosymmetric phases and hence uninterpretable maps.	2	23.68	67366	67366	3423	98.4	0.166	0.166	0.1592	0.205	0.199	RANDOM	19.8

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]
-3.66			2.23		1.43

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.8
c_scangle_it	3.09
c_scbond_it	2.25
c_angle_deg	2.1
c_mcangle_it	1.81
c_improper_angle_d	1.37
c_mcbond_it	1.28
c_bond_d	0.024

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5796
Nucleic Acid Atoms
Solvent Atoms	781
Heterogen Atoms	43

Software

Software
Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing