1IM5 | pdb_00001im5

Crystal Structure of Pyrazinamidase of Pyrococcus horikoshii in Complex with Zinc

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		a structure obtained on MAD data

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	27.5% peg 3350, 100mM sodium acetate, pH 4.6, 250 mM ammonium acetate, 8% glycerol. Seeding., VAPOR DIFFUSION, HANGING DROP, temperature 298K
2	VAPOR DIFFUSION, HANGING DROP	4.6	298	peg 3350, ammonium acetate, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.978	α = 90
b = 43.266	β = 101.34
c = 55.553	γ = 90

Symmetry
Space Group	P 1 21 1

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	mirrors	2000-05-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.2	1.00	ALS	5.0.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.65	20	97.3	0.036	37.8	3.11	18550	18049			16.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.65	1.68	81.9		0.064	25.5	2.02	753

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 (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	MOLECULAR REPLACEMENT	FREE R	a structure obtained on MAD data	1.65	20	18533	17977	1775	97	0.1529	0.1529	0.1527	0.15	0.2323	0.22	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		1552

RMS Deviations
Key	Refinement Restraint Deviation
s_non_zero_chiral_vol	0.05
s_similar_adp_cmpnt	0.05
s_zero_chiral_vol	0.03
s_from_restr_planes	0.025
s_angle_d	0.02
s_bond_d
s_similar_dist
s_anti_bump_dis_restr
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1437
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	1

Software

Software
Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
SOLVE	phasing
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.