3FUC | pdb_00003fuc

Recombinant calf purine nucleoside phosphorylase in a binary complex with multisubstrate analogue inhibitor 9-(5',5'-difluoro-5'-phosphonopentyl)-9-deazaguanine structure in a new space group with one full trimer in the asymmetric unit

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.7	298	33% PEG 400, 0.1M SODIUM AZIDE, 0.1M HEPES, 0.1M MAGNESIUM CHLORIDE, 1% OCTYL BETA-D-GLUCOPYRANOSIDE, pH 7.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.795	α = 90
b = 78.253	β = 97.19
c = 94.901	γ = 90

Symmetry
Space Group	C 1 2 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	MARRESEARCH	BENT MIRROR	2007-08-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.0500	MPG/DESY, HAMBURG	BW6

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	1.45	10	99.4	0.082	4.4	3.3	173360	173360			16

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	1.45	1.53	99.9		0.236	3	2.6	25329

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 Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1LVU	1.45	10	173360	173360	8787	99.31	0.18095	0.18095	0.17999	0.19	0.19933	THIN RESIOLUTION SHELLS	16.41

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]
-0.05		0.13	-0.26		0.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.674
r_dihedral_angle_4_deg	17.384
r_dihedral_angle_3_deg	13.148
r_dihedral_angle_1_deg	5.847
r_angle_other_deg	3.683
r_scangle_it	3.264
r_scbond_it	2.071
r_angle_refined_deg	1.386
r_mcangle_it	1.369
r_mcbond_it	0.782
r_symmetry_vdw_refined	0.331
r_symmetry_vdw_other	0.27
r_nbd_other	0.246
r_nbd_refined	0.21
r_nbtor_refined	0.179
r_nbtor_other	0.106
r_xyhbond_nbd_refined	0.103
r_chiral_restr	0.093
r_symmetry_hbond_refined	0.062
r_bond_refined_d	0.012
r_gen_planes_other	0.007
r_symmetry_metal_ion_refined	0.007
r_gen_planes_refined	0.006
r_metal_ion_refined	0.004
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6456
Nucleic Acid Atoms
Solvent Atoms	447
Heterogen Atoms	72

Software

Software
Software Name	Purpose
MAR345	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling