3EQU | pdb_00003equ

Crystal structure of penicillin-binding protein 2 from Neisseria gonorrhoeae

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	2.2 M ammonium sulphate, 100 mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.8	67.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.4	α = 90
b = 138.6	β = 90
c = 228	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	ADSC QUANTUM 4		2001-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	1.00	SSRL	BL9-2

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	2.3	87	90.3	0.061	8.8	6.2	73860	73860			43.2

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)
1	2.3	2.36	52.6		0.349		3.7	3081

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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		THROUGHOUT	2.4	66.6	68535	68535	3467	94.6	0.211	0.211	0.209	0.2335	0.237	0.2611	RANDOM	36.7

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]
-2.52			1.25		1.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.7
r_dihedral_angle_4_deg	20.7
r_dihedral_angle_3_deg	17.5
r_dihedral_angle_1_deg	6.3
r_scangle_it	3.218
r_scbond_it	2.097
r_angle_refined_deg	1.45
r_mcangle_it	1.185
r_mcbond_it	0.862
r_nbtor_refined	0.297
r_nbd_refined	0.203
r_symmetry_vdw_refined	0.173
r_symmetry_hbond_refined	0.162
r_xyhbond_nbd_refined	0.135
r_chiral_restr	0.097
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6516
Nucleic Acid Atoms
Solvent Atoms	146
Heterogen Atoms	97

Software

Software
Software Name	Purpose
Blu-Ice	data collection
SOLVE	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling