1RYA | pdb_00001rya

Crystal Structure of the E. coli GDP-mannose mannosyl hydrolase in complex with GDP and MG

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	20% PEG 4000, 0.2M Na (or Mg) Acetate, 0.1M Tris HCl pH8.5), VAPOR DIFFUSION, SITTING DROP

Crystal Properties
Matthews coefficient	Solvent content
2.73	55.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.069	α = 90
b = 81.363	β = 90
c = 98.974	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	180	CCD	ADSC QUANTUM 4			M	SINGLE WAVELENGTH
2	1		IMAGE PLATE	RIGAKU RAXIS IV

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X6A	0.9791	NSLS	X6A
2	ROTATING ANODE	RIGAKU RU200	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	63.25	92.41	0.093	38.2		88143	88143

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.298	1.332	73.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MIR	THROUGHOUT	1.3	63.25	88143	4715	92.41	0.16994	0.16882	0.19059	RANDOM	11.643

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]
0.26			-0.23		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.737
r_scangle_it	3.016
r_scbond_it	1.967
r_angle_refined_deg	1.557
r_mcangle_it	1.416
r_angle_other_deg	0.847
r_mcbond_it	0.77
r_symmetry_vdw_other	0.367
r_nbd_other	0.261
r_nbd_refined	0.217
r_symmetry_hbond_refined	0.19
r_xyhbond_nbd_refined	0.146
r_symmetry_vdw_refined	0.145
r_chiral_restr	0.088
r_nbtor_other	0.081
r_gen_planes_other	0.016
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_bond_other_d	0.002
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_refined
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	2606
Nucleic Acid Atoms
Solvent Atoms	727
Heterogen Atoms	75

Software

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