2OQC

Crystal Structure of Penicillin V acylase from Bacillus subtilis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.2	291	4M sodium formate in 100mM Tris-HCl buffer, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.963	α = 90
b = 307.956	β = 90
c = 56.003	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	RIGAKU RAXIS IV	MIRRORS	2002-09-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.497	20					31859			40.76

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.497	2.562	96.24

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 2PVA	2.5	20	31859	1705	98.65	0.15785	0.15466	0.2179	RANDOM	40.756

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]
0.01			-3.35		3.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.708
r_dihedral_angle_4_deg	22.909
r_dihedral_angle_3_deg	19.579
r_dihedral_angle_1_deg	7.424
r_scangle_it	6.476
r_scbond_it	4.238
r_mcangle_it	2.604
r_angle_refined_deg	2.341
r_mcbond_it	1.627
r_symmetry_hbond_refined	0.396
r_nbtor_refined	0.322
r_symmetry_vdw_refined	0.296
r_nbd_refined	0.263
r_xyhbond_nbd_refined	0.227
r_chiral_restr	0.182
r_bond_refined_d	0.03
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5082
Nucleic Acid Atoms
Solvent Atoms	420
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing