3UMB | pdb_00003umb

Crystal Structure of the L-2-Haloacid Dehalogenase RSc1362

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QH9	PDB ENTRY 1QH9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	298	15% isopropanol, 0.1 M potassium chloride, 25 mM magnesium chloride, 2% 1,4-dioxane, 50 mM sodium cacodylate, pH 6.0, cryoprotectant: Paratone N, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.25	45.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.38	α = 90
b = 129.57	β = 90
c = 54.3	γ = 90

Symmetry
Space Group	C 2 2 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	IMAGE PLATE	RIGAKU	Varimax optics	2010-05-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.2	64.785	99.9	0.043	26.2	7	12258	12258

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	2.2	2.32	100		0.214	0.214	3.5	7	1754

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1QH9	2.2	24.67	12255	585	99.85	0.2328	0.2302	0.229	0.2828	0.2782	RANDOM	33.9067

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]
0.82			-1.53		0.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.694
r_dihedral_angle_3_deg	16.82
r_dihedral_angle_4_deg	15.977
r_dihedral_angle_1_deg	6.821
r_scangle_it	3.377
r_scbond_it	2.282
r_angle_refined_deg	1.609
r_mcangle_it	1.573
r_angle_other_deg	0.978
r_mcbond_it	0.855
r_mcbond_other	0.166
r_chiral_restr	0.094
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1751
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	8

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing