1M3U | pdb_00001m3u

Crystal Structure of Ketopantoate Hydroxymethyltransferase complexed the Product Ketopantoate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Initial C-alpha trace obtained from 3.0 A selenomethionine MAD-phased maps of a different crystal form: P21, cell=(87.8,155.4,209.9,90,99.3,90)

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.8	277	PEG 8000, sodium chloride, sodium acetate, sodium citrate buffer, pH 6.8, VAPOR DIFFUSION, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.38	48.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.074	α = 90
b = 157.17	β = 97.44
c = 100.181	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	SBC-2	mirror	1999-08-26	M	MAD
2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97927, 0.9393, 0.979	APS	19-ID

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	1.8	75	94.2	0.083	0.083	12.9	4.5	229086	229086		1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.9	75		0.527	0.527	2.4	3.5	26449

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	THROUGHOUT	Initial C-alpha trace obtained from 3.0 A selenomethionine MAD-phased maps of a different crystal form: P21, cell=(87.8,155.4,209.9,90,99.3,90)	1.8	100	-1	-1	224262	224262	4812	94.12	0.15844	0.15276	0.15193	0.16	0.19258	0.2	random	22.888

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]
0.47		-0.37	0.27		-0.83

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	13.928
r_dihedral_angle_1_deg	5.983
r_scangle_it	3.715
r_scbond_it	2.31
r_angle_refined_deg	1.548
r_mcangle_it	1.403
r_angle_other_deg	0.88
r_mcbond_it	0.791
r_symmetry_vdw_other	0.255
r_nbd_other	0.237
r_symmetry_hbond_refined	0.224
r_nbd_refined	0.212
r_xyhbond_nbd_refined	0.182
r_symmetry_vdw_refined	0.128
r_chiral_restr	0.092
r_nbtor_other	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_xyhbond_nbd_other
r_symmetry_hbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19602
Nucleic Acid Atoms
Solvent Atoms	2776
Heterogen Atoms	110

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SnB	phasing
SHARP	phasing
REFMAC	refinement
CCP4	data scaling