8HFW | pdb_00008hfw

The crystal structure of alpha/beta fold hydrolase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5Y57

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	289	0.1 M Bis-Tris, pH7.2, 0.2 M Magnesium acetate, 17% PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 166.96	α = 90
b = 68.41	β = 93.575
c = 75.34	γ = 90

Symmetry
Space Group	C 1 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	298	PIXEL	DECTRIS EIGER2 S 9M		2021-10-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL02U1	0.979	SSRF	BL02U1

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	1.66	57.64	98.38	0.048	0.999	19.8	6.37		98523

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.66	1.7			0.466	0.523	0.999

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 (All)	R-Work (Depositor)	R-Free (Depositor)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	5Y57	1.66	57.638	98506	4917	98.38	0.195	0.1936	0.2287	27.202

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]
0.227		0.578	-0.983		0.679

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.472
r_dihedral_angle_3_deg	14.84
r_dihedral_angle_1_deg	5.379
r_rigid_bond_restr	5.374
r_lrange_it	4.26
r_lrange_other	4.25
r_scangle_it	3.753
r_scangle_other	3.753
r_dihedral_angle_2_deg	3.461
r_mcangle_it	3.322
r_mcangle_other	3.322
r_scbond_it	3.268
r_scbond_other	3.268
r_mcbond_it	2.732
r_mcbond_other	2.732
r_angle_refined_deg	1.478
r_angle_other_deg	0.449
r_symmetry_nbd_refined	0.238
r_nbd_refined	0.229
r_symmetry_nbd_other	0.191
r_nbtor_refined	0.179
r_nbd_other	0.129
r_symmetry_xyhbond_nbd_refined	0.122
r_xyhbond_nbd_refined	0.109
r_symmetry_nbtor_other	0.074
r_chiral_restr	0.065
r_bond_refined_d	0.008
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	5979
Nucleic Acid Atoms
Solvent Atoms	329
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
BALBES	phasing