1K5S | pdb_00001k5s

PENICILLIN ACYLASE, MUTANT COMPLEXED WITH PPA

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, PPA, pH 7.20, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.82	α = 72.89
b = 64.36	β = 74.01
c = 64.75	γ = 73.55

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	MAC Science DIP-2020	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	2.43	30	96.2	0.037	21.1	2.185	27684	26632		-3

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)
	2.43	2.47	95.7		0.066	10.9

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1PNK	2.43	30	26632	1375	96.2	0.194	0.173	0.233	RANDOM	18.104

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]
-0.44	0.06	-0.23	0.14	-0.36	0.6

RMS Deviations
Key	Refinement Restraint Deviation
p_scangle_it	2.261
p_scbond_it	1.569
p_angle_d	1.131
p_mcangle_it	1.049
p_mcbond_it	0.629
p_hb_or_metal_coord	0.215
p_xyhbond_nbd	0.139
p_chiral_restr	0.075
p_bond_d	0.009
p_plane_restr	0.004
p_angle_deg
p_planar_d
p_singtor_nbd
p_multtor_nbd
p_xhyhbond_nbd
p_planar_tor
p_staggered_tor
p_orthonormal_tor
p_transverse_tor
p_special_tor

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6067
Nucleic Acid Atoms
Solvent Atoms	360
Heterogen Atoms	12

Software

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