4CKC | pdb_00004ckc

Vaccinia virus capping enzyme complexed with SAH (monoclinic form)

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5		PROTEIN SOLUTION AT 4 MG/ML IN 40 MM TRIS-HCL, PH 8.0, 200 MM NACL, 5 MM DTT WITH 5 MM ADOMET. RESERVOIR SOLUTION: 0.1 M TRIS-HCL, PH 7.5, 0.2 M LICL, 0.2M (NH4)2SO4, 15% PEG4000

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.6

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.71	α = 90
b = 200.26	β = 102.18
c = 128.1	γ = 90

Symmetry
Space Group	P 1 21 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		2004-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14		ESRF	BM14

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	2.9	50	92	0.14	5.05	1.88		62825

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	2.9	2.97	81.1		0.4	2.13	1.83

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 2VDW	2.9	125	59652	3174	93.55	0.25697	0.25485	0.26	0.29706	0.3	RANDOM	42.427

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]
-1.57		0.52	-3.01		3.98

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.478
r_dihedral_angle_4_deg	16.253
r_dihedral_angle_3_deg	16.218
r_dihedral_angle_1_deg	6.341
r_long_range_B_refined	2.468
r_long_range_B_other	2.468
r_mcangle_it	1.469
r_mcangle_other	1.469
r_angle_refined_deg	1.01
r_scangle_other	0.809
r_mcbond_it	0.78
r_mcbond_other	0.78
r_angle_other_deg	0.699
r_scbond_it	0.382
r_scbond_other	0.382
r_chiral_restr	0.055
r_bond_refined_d	0.005
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17909
Nucleic Acid Atoms
Solvent Atoms	82
Heterogen Atoms	52

Software

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