2C5A

GDP-mannose-3', 5' -epimerase (Arabidopsis thaliana),Y174F, with GDP-beta-L-galactose bound in the active site

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2C54	PDB ENTRY 2C54

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6		100 MM BIS-TRIS PH 6.0, 2.2M AMMONIUM SULPHATE, SITTING DROP, VAPOUR DIFFUSION. CRYOPROTECTED 6 M SODIUM FORMATE.

Crystal Properties
Matthews coefficient	Solvent content
1.99	38.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 62.497	α = 90
b = 83.273	β = 98.89
c = 66.12	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	ADSC CCD		2005-05-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2		ESRF	ID14-2

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	1.4	23.12	96.7	0.05	17.9	3.6		126826			11

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	1.4	1.48	95.4		0.23	5.5	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 2C54	1.4	21.61	126798	6337	96.5	0.105	0.103	0.14	RANDOM	9.78

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]
-0.262		-0.05	0.589		-0.342

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.509
r_dihedral_angle_4_deg	21.328
r_dihedral_angle_3_deg	12.532
r_dihedral_angle_1_deg	6.407
r_scangle_it	4.774
r_scbond_it	3.673
r_mcangle_it	2.518
r_mcbond_it	2.188
r_angle_refined_deg	1.921
r_angle_other_deg	1.086
r_symmetry_vdw_other	0.283
r_nbd_refined	0.23
r_xyhbond_nbd_refined	0.227
r_symmetry_hbond_refined	0.225
r_chiral_restr	0.217
r_nbd_other	0.208
r_symmetry_vdw_refined	0.191
r_nbtor_refined	0.186
r_nbtor_other	0.089
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5786
Nucleic Acid Atoms
Solvent Atoms	1018
Heterogen Atoms	231

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling