1Q6R | pdb_00001q6r

Structure of 3-keto-L-gulonate 6-phosphate decarboxylase with bound L-xylulose 5-phosphate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7	298	16% MePEG 2000, 50 mM BTP pH 7.0, 5 mM MgCl2, microbatch, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.13	41.8

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.912	α = 90
b = 41.58	β = 96.41
c = 91.627	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		2002-12-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.9870	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.76	100	98.2	18.1			45531		2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.76	1.82	98.1		2.62

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 (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	1.76	91.29	45531	43255	2276	97.97	0.1915	0.18954	0.1981	0.22875	0.2352	RANDOM	26.359

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]
-0.63		0.53	1.51		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.203
r_scangle_it	4.95
r_scbond_it	3.059
r_mcangle_it	1.973
r_angle_refined_deg	1.724
r_angle_other_deg	1.685
r_mcbond_it	1.086
r_symmetry_vdw_other	0.272
r_nbd_other	0.248
r_nbd_refined	0.233
r_symmetry_hbond_refined	0.218
r_symmetry_vdw_refined	0.189
r_xyhbond_nbd_refined	0.164
r_chiral_restr	0.101
r_nbtor_other	0.083
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
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	3267
Nucleic Acid Atoms
Solvent Atoms	303
Heterogen Atoms	28

Software

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