2D4M | pdb_00002d4m

Crystal Structure of apo M-PMV dUTPase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2D4L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	PEG 8000, AMMONIUM CHLORIDE, TRIS, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.11	41.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.191	α = 90
b = 61.191	β = 90
c = 63.31	γ = 120

Symmetry
Space Group	P 63

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	mirrors	2004-12-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.8031	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.83	53	97.37	0.091	0.074	8.85	2.74	11637	11637		-3	33.38

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.83	1.94	95.04		0.503	0.4	2.66	2.54	1804

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		THROUGHOUT	2D4L	1.85	20	10739	10739	611	98.01	0.16194	0.16194	0.16022	0.1794	0.19193	0.2136	RANDOM	32.784

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]
1.1	0.55		1.1		-1.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.375
r_dihedral_angle_4_deg	20.842
r_dihedral_angle_3_deg	13.386
r_dihedral_angle_1_deg	12.098
r_scangle_it	11.383
r_scbond_it	8.758
r_mcangle_it	4.382
r_mcbond_it	3.232
r_angle_refined_deg	1.862
r_nbtor_refined	0.319
r_nbd_refined	0.23
r_symmetry_vdw_refined	0.213
r_xyhbond_nbd_refined	0.187
r_symmetry_hbond_refined	0.148
r_chiral_restr	0.123
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	812
Nucleic Acid Atoms
Solvent Atoms	147
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data scaling