3KWM

Crystal structure of ribose-5-isomerase A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ENQ	PDB entry 3ENQ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	0.2M Lithium Chloride, 0.1M Tris, 20% PEG 6000 , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.97

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 182.36	α = 90
b = 73.085	β = 90
c = 75.303	γ = 90

Symmetry
Space Group	P 21 21 2

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 210r		2009-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.97918	APS	19-BM

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	2.3	50	98.2	0.09	0.09	24.075	6.4		1052731		-3

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	2.3	2.34	71.2		0.566	0.566	2.356	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 3ENQ	2.32	38.68	45501	40018	2128	94.49	0.17252	0.16997	0.2211	RANDOM	17.354

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]
-0.5			0.44		0.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	42.206
r_dihedral_angle_3_deg	13.949
r_dihedral_angle_4_deg	13.009
r_dihedral_angle_1_deg	5.828
r_scangle_it	1.685
r_angle_refined_deg	1.101
r_scbond_it	0.994
r_mcangle_it	0.534
r_nbtor_refined	0.296
r_mcbond_it	0.273
r_nbd_refined	0.181
r_symmetry_vdw_refined	0.17
r_xyhbond_nbd_refined	0.13
r_metal_ion_refined	0.112
r_symmetry_hbond_refined	0.102
r_chiral_restr	0.067
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	6640
Nucleic Acid Atoms
Solvent Atoms	404
Heterogen Atoms	51

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling