2VBT | pdb_00002vbt

Riboflavin kinase Mj0056 from Methanocaldococcus jannaschii in complex with CDP and PO4

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				40% V/V ETHYLENE GLYCOL, 100 MM PHOSPHATE-CITRATE PH 4.2, 200 MM NH4SO4

Crystal Properties
Matthews coefficient	Solvent content
5.3	76.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 77.72	α = 90
b = 77.72	β = 90
c = 106.868	γ = 90

Symmetry
Space Group	P 43 21 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	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	2.7	38.32	99.5	0.08	16.57	5.5		9448

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	2.7	2.87	98.1		0.92	2.02	5.6

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 2VBS	2.7	20	8971	453	99.7	0.211	0.209	0.22	0.266	0.28	RANDOM	60.53

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]
2.32			2.32		-4.64

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.962
r_dihedral_angle_3_deg	16.911
r_dihedral_angle_4_deg	8.991
r_dihedral_angle_1_deg	6.337
r_angle_other_deg	3.937
r_scangle_it	2.547
r_mcangle_it	1.738
r_angle_refined_deg	1.476
r_scbond_it	1.464
r_mcbond_it	0.932
r_nbd_other	0.225
r_symmetry_vdw_refined	0.213
r_nbd_refined	0.205
r_nbtor_refined	0.191
r_symmetry_vdw_other	0.16
r_xyhbond_nbd_refined	0.151
r_nbtor_other	0.111
r_chiral_restr	0.079
r_bond_refined_d	0.014
r_gen_planes_other	0.005
r_gen_planes_refined	0.004
r_bond_other_d
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_refined
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	1105
Nucleic Acid Atoms
Solvent Atoms	31
Heterogen Atoms	31

Software

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