3L5K

The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PIB	2PIB, 3HLT, 3K1Z, 2W4M
experimental model	PDB	3HLT	2PIB, 3HLT, 3K1Z, 2W4M
experimental model	PDB	3K1Z	2PIB, 3HLT, 3K1Z, 2W4M
experimental model	PDB	2W4M	2PIB, 3HLT, 3K1Z, 2W4M

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	0.1 M Sodium dihydrogen phosphate, 1.344 M di-potassium hydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.86	68.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 85.19	α = 90
b = 85.19	β = 90
c = 103.03	γ = 120

Symmetry
Space Group	P 31 2 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	MARMOSAIC 225 mm CCD		2009-10-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9795	Diamond	I02

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	42.59	99.5	0.107	0.107	9.4	4.1		29508

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)
	2	2.11	99		0.855	0.855	2	4.2	17548

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	2PIB, 3HLT, 3K1Z, 2W4M	2	42.6	28009	28009	1495	99.13	0.1677	0.1677	0.16542	0.21272	RANDOM	15.171

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]
0.81	0.4		0.81		-1.21

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.768
r_dihedral_angle_4_deg	24.654
r_dihedral_angle_3_deg	15.046
r_scangle_it	12.04
r_scbond_it	10.269
r_mcangle_it	6.212
r_dihedral_angle_1_deg	5.267
r_mcbond_it	4.763
r_mcbond_other	2.013
r_angle_refined_deg	1.61

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.768
r_dihedral_angle_4_deg	24.654
r_dihedral_angle_3_deg	15.046
r_scangle_it	12.04
r_scbond_it	10.269
r_mcangle_it	6.212
r_dihedral_angle_1_deg	5.267
r_mcbond_it	4.763
r_mcbond_other	2.013
r_angle_refined_deg	1.61
r_angle_other_deg	0.967
r_chiral_restr	0.098
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1835
Nucleic Acid Atoms
Solvent Atoms	217
Heterogen Atoms	11

Software

Software
Software Name	Purpose
MAR345	data collection
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.