1MZV

Crystal Structure of Adenine Phosphoribosyltransferase (APRT) From Leishmania tarentolae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QB7	PDB ENTRY 1QB7

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7	277	MOPS 100 mM, 22% isopropanol, Protein at 8 mg/ml, pH 7.00, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.75

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.538	α = 90
b = 64.538	β = 90
c = 234.44	γ = 120

Symmetry
Space Group	P 61 2 2

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	MARRESEARCH		1999-08-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1		LNLS	D03B-MX1

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	2.2	28.27	99.5				15513

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	2.2	2.24	93.1

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 (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	THROUGHOUT	PDB ENTRY 1QB7	2.2	28.27	15513	14724	789	99.5	0.183	0.181	0.19	0.218	0.23	RANDOM	24.16

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]
2.01	1.01		2.01		-3.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.99
r_dihedral_angle_3_deg	16.767
r_dihedral_angle_4_deg	11.577
r_dihedral_angle_1_deg	6.619
r_scangle_it	3.251
r_scbond_it	1.952
r_angle_refined_deg	1.494
r_mcangle_it	1.231
r_angle_other_deg	0.871
r_mcbond_it	0.653
r_symmetry_vdw_other	0.368
r_symmetry_hbond_refined	0.274
r_nbd_other	0.25
r_xyhbond_nbd_refined	0.233
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.174
r_chiral_restr	0.094
r_nbtor_other	0.086
r_bond_refined_d	0.014
r_gen_planes_other	0.007
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_xyhbond_nbd_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	1650
Nucleic Acid Atoms
Solvent Atoms	233
Heterogen Atoms	28

Software

Software
Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction