1XBV | pdb_00001xbv

Crystal structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound D-ribulose 5-phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	16% PEG 5000 methyl ether, 100 mM BTP, 5 mM MgCl2, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.814	α = 90
b = 41.471	β = 96.65
c = 91.184	γ = 90

Symmetry
Space Group	C 1 2 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	CUSTOM-MADE		2004-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.961	APS	19-ID

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	1.66	92	99.1	0.042	15.8		382817	382817		2

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)
	1.66	1.72	98.2		0.4377	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MOLECULAR REPLACEMENT	THROUGHOUT	1.66	91.29	51641	51641	2762	99.07	0.16392	0.16392	0.16226	0.1758	0.1939	0.2067	RANDOM	20.559

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		0.83	1.39		-0.73

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.302
r_scangle_it	5.496
r_scbond_it	3.773
r_mcangle_it	2.725
r_mcbond_it	1.719
r_angle_refined_deg	1.648
r_angle_other_deg	1.152
r_symmetry_vdw_other	0.301
r_nbd_other	0.251
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.197
r_xyhbond_nbd_refined	0.186
r_chiral_restr	0.107
r_metal_ion_refined	0.105
r_symmetry_vdw_refined	0.101
r_nbtor_other	0.084
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.003
r_gen_planes_other	0.003
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3286
Nucleic Acid Atoms
Solvent Atoms	425
Heterogen Atoms	28

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing