4K9C | pdb_00004k9c

CRYSTAL STRUCTURE OF probable sugar kinase protein from Rhizobium etli CFN 42 complexed with N-(HYDROXYMETHYL)BENZAMIDE and 4-METHYL-3,4-DIHYDRO-2H-1,4-BENZOXAZINE-7-CARBOXYLIC ACID

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E3A	PDB ENTRY 4E3A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	298	0.2M AMMONIUM ACETATE, 0.1M BIS:TRIS:HCL, PH 6.5,25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.165	α = 90
b = 81.355	β = 98.08
c = 82.69	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	ADSC QUANTUM 315		2013-03-28		SAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	1.075	NSLS	X29A

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	1.49	50	95	0.072	9.5	2.5		103798

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.52	96.4			2.1

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 4E3A	1.5	40.09	96601	5124	94.95	0.17431	0.17322	0.17	0.19477	0.19	RANDOM	22.805

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]
-0.13		0.04	0.09		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.891
r_sphericity_free	30.844
r_dihedral_angle_4_deg	14.253
r_dihedral_angle_3_deg	12.842
r_sphericity_bonded	9.946
r_dihedral_angle_1_deg	5.23
r_rigid_bond_restr	1.489
r_angle_refined_deg	1.19
r_chiral_restr	0.078
r_bond_refined_d	0.006
r_gen_planes_refined	0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5008
Nucleic Acid Atoms
Solvent Atoms	423
Heterogen Atoms	106

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction