1Q6Q | pdb_00001q6q

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

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	7	298	15% 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 = 123.182	α = 90
b = 41.727	β = 95.87
c = 92.125	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	ADSC QUANTUM 4		2003-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 14-BM-C	0.987	APS	14-BM-C

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	1.695	100	95.4	27.8			49427		2.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.695	1.75	82.8		5.8

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	1.695	91.29	49427	47189	2538	95.2	0.1735	0.17177	0.1835	0.20656	0.2187	RANDOM	20.917

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]
-1.16		0.45	1.14		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.402
r_scangle_it	5.259
r_scbond_it	3.642
r_mcangle_it	2.726
r_mcbond_it	1.783
r_angle_refined_deg	1.701
r_angle_other_deg	1.32
r_symmetry_vdw_other	0.294
r_nbd_other	0.246
r_nbd_refined	0.221
r_symmetry_vdw_refined	0.192
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.168
r_chiral_restr	0.122
r_nbtor_other	0.085
r_bond_refined_d	0.02
r_gen_planes_refined	0.009
r_gen_planes_other	0.007
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	3276
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
CNS	phasing