2JCM | pdb_00002jcm

Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with beryllium trifluoride

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2J2C	PDB ENTRY 2J2C

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		1.8 M MAGNESIUM SULFATE, 0.1 M TRIS PH 8.5

Crystal Properties
Matthews coefficient	Solvent content
3.16	61.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.48	α = 90
b = 128.26	β = 90
c = 131.01	γ = 90

Symmetry
Space Group	I 2 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	CCD	ADSC CCD	MIRRORS	2006-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4		ESRF	ID14-4

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	2.15	20	98	0.16	7.14	5.2		41406		-3

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	2.15	2.2	99.8		0.5	3.36	5.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 2J2C	2.15	20.67	39316	2089	98.1	0.213	0.21	0.22	0.266	0.27	RANDOM	13.27

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]
-0.45			-0.47		0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.187
r_dihedral_angle_4_deg	16.755
r_dihedral_angle_3_deg	15.654
r_dihedral_angle_1_deg	6.557
r_scangle_it	3.526
r_scbond_it	2.385
r_angle_refined_deg	1.759
r_mcangle_it	1.449
r_mcbond_it	0.916
r_nbtor_refined	0.313
r_nbd_refined	0.21
r_symmetry_vdw_refined	0.199
r_xyhbond_nbd_refined	0.153
r_symmetry_hbond_refined	0.152
r_chiral_restr	0.117
r_bond_refined_d	0.019
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3812
Nucleic Acid Atoms
Solvent Atoms	260
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing