2QLX

Crystal structure of rhamnose mutarotase RhaU of Rhizobium leguminosarum in complex with L-Rhamnose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2QLW	PDB entry 2QLW

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	298	2M Sodium Formate, 0.1M Sodium Acetate pH 4.6, 20% Glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.84

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.652	α = 90
b = 68.652	β = 90
c = 100.719	γ = 120

Symmetry
Space Group	P 32 1 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 4	MIRRORS	2006-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	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	1.85	30	98.3	0.093		4.2	23317	23317

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	1.85	1.92	92.5		0.322	3.7	2.8	2169

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 2QLW	2	28.51	18417	18417	942	99.04	0.138	0.138	0.135	0.188	RANDOM	16.591

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.064
r_dihedral_angle_4_deg	18.664
r_dihedral_angle_3_deg	14.36
r_dihedral_angle_1_deg	5.452
r_scangle_it	4.393
r_scbond_it	3.093
r_angle_other_deg	1.86
r_mcangle_it	1.82
r_angle_refined_deg	1.777
r_mcbond_it	1.511
r_mcbond_other	0.341
r_symmetry_vdw_refined	0.3
r_nbd_refined	0.238
r_nbd_other	0.21
r_symmetry_vdw_other	0.192
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.184
r_symmetry_hbond_refined	0.181
r_chiral_restr	0.144
r_nbtor_other	0.096
r_bond_refined_d	0.021
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1748
Nucleic Acid Atoms
Solvent Atoms	204
Heterogen Atoms	69

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
MOLREP	phasing