2VBV

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and FMN

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				20% W/V PEG 8000, 200 MM SODIUM IODIDE

Crystal Properties
Matthews coefficient	Solvent content
2.6	52.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.482	α = 90
b = 73.299	β = 90
c = 104.907	γ = 90

Symmetry
Space Group	P 21 21 21

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA		SLS	X10SA

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	2.4	38.58	98.6	0.13	8.67	5.5		12903

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	2.4	2.55	98.5		0.69	2.25	5.62

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VBT	2.4	20	12202	644	100	0.232	0.227	0.323	RANDOM	42.39

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]
0.84			2.41		-3.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.186
r_dihedral_angle_3_deg	20.516
r_dihedral_angle_4_deg	14.065
r_dihedral_angle_1_deg	8.057
r_angle_other_deg	4.036
r_scangle_it	2.951
r_scbond_it	1.814
r_angle_refined_deg	1.7
r_mcangle_it	1.406
r_mcbond_it	0.757
r_nbd_other	0.23
r_nbd_refined	0.225
r_xyhbond_nbd_refined	0.223
r_symmetry_vdw_other	0.209
r_nbtor_refined	0.196
r_symmetry_vdw_refined	0.184
r_nbtor_other	0.114
r_symmetry_hbond_refined	0.102
r_chiral_restr	0.088
r_bond_refined_d	0.015
r_gen_planes_other	0.007
r_gen_planes_refined	0.005
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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	2178
Nucleic Acid Atoms
Solvent Atoms	73
Heterogen Atoms	85

Software

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