1RXY | pdb_00001rxy

E. coli uridine phosphorylase: type-B native

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LGG	TYPE-A NATIVE (1LGG)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	TRIS HCL, PEG4000, POTASSIUM ACETATE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.25	44.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 152.928	α = 90
b = 152.928	β = 90
c = 50.864	γ = 120

Symmetry
Space Group	H 3

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	ADSC QUANTUM 4		1999-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X26C	1.10	NSLS	X26C

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	1.7	16.54	99.9	0.053	9.7	5.4	48715	48715			21.544

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	1.7	1.79	99.9		0.337	2.2	5.1	7095

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	TYPE-A NATIVE (1LGG)	1.7	16.1	46224	46224	2478	99.98	0.13002	0.12819	0.14	0.16442	0.18	RANDOM	12.299

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]
0.03	0.02		0.03		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.944
r_scangle_it	2.334
r_scbond_it	1.562
r_angle_refined_deg	1.547
r_angle_other_deg	1.264
r_mcangle_it	1.109
r_mcbond_it	0.683
r_symmetry_vdw_other	0.312
r_nbd_other	0.235
r_nbd_refined	0.214
r_symmetry_hbond_refined	0.209
r_chiral_restr	0.168
r_xyhbond_nbd_refined	0.154
r_symmetry_vdw_refined	0.098
r_nbtor_other	0.078
r_metal_ion_refined	0.031
r_bond_refined_d	0.016
r_gen_planes_refined	0.006
r_gen_planes_other	0.005
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_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	3703
Nucleic Acid Atoms
Solvent Atoms	415
Heterogen Atoms	28

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling