5LDR

Crystal structure of a cold-adapted dimeric beta-D-galactosidase from Paracoccus sp. 32d strain in complex with galactose

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5EUV

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	293	24% PEG 2000 0.2M ammonium acetate 0.1M Bis-Tris pH 5.0

Crystal Properties
Matthews coefficient	Solvent content
2.62	53.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.26	α = 90
b = 107.58	β = 90
c = 201.55	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	100	PIXEL	DECTRIS PILATUS3 S 6M	mirrors	2013-12-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	1.017	EMBL/DESY, HAMBURG	X13

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	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	3.15	50	96.7	0.176	0.983	7.77	3.65		29579

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3.15	3.25	94.4		0.848	0.643	1.63	3.64

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	5EUV	3.15	46.27	28097	1480	96.68	0.18806	0.18394	0.26658	RANDOM	62.444

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]
-3.61			6.47		-2.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.192
r_dihedral_angle_4_deg	19.726
r_dihedral_angle_3_deg	19.29
r_long_range_B_refined	12.346
r_long_range_B_other	12.346
r_dihedral_angle_1_deg	9.226
r_mcangle_it	8.215
r_mcangle_other	8.215
r_scangle_other	7.996
r_mcbond_it	5.177
r_mcbond_other	5.174
r_scbond_it	4.962
r_scbond_other	4.962
r_angle_refined_deg	2.091
r_angle_other_deg	1.172
r_chiral_restr	0.1
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.002
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	11527
Nucleic Acid Atoms
Solvent Atoms	114
Heterogen Atoms	83

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing