1K7D

Penicillin Acylase with Phenyl Proprionic Acid

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PNK	PDB ENTRY 1PNK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.2	277	MOPS BUFFER, PEG MME 2K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.331	α = 72.54
b = 64.551	β = 73.29
c = 64.347	γ = 73.58

Symmetry
Space Group	P 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	IMAGE PLATE	MACSCIENCE	mirrors	2000-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	ENRAF-NONIUS FR591	1.5418

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	2.15	30	95.3	0.068	10.1	1.74	40070	38187		-3	34.5

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)
1	2.15	2.19	87.5		0.229	2.7

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 1PNK	2.15	30.15	36555	1632	91.2	0.18376	0.18215	0.21646	RANDOM	22.081

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]
-0.47	-0.3	0.05	-0.04	-0.04	0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.201
r_dihedral_angle_1_deg	4.07
r_scangle_it	3.429
r_scbond_it	2.15
r_angle_refined_deg	1.589
r_mcangle_it	1.347
r_angle_other_deg	0.88
r_mcbond_it	0.75
r_symmetry_vdw_refined	0.454
r_symmetry_hbond_refined	0.371
r_nbd_refined	0.238
r_nbd_other	0.214
r_symmetry_vdw_other	0.214
r_xyhbond_nbd_refined	0.168
r_nbtor_other	0.124
r_metal_ion_refined	0.098
r_chiral_restr	0.097
r_xyhbond_nbd_other	0.02
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_metal_ion_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6072
Nucleic Acid Atoms
Solvent Atoms	319
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
TRUNCATE	data reduction
CNS	refinement
DENZO	data reduction
CCP4	data scaling
CNS	phasing