29LY | pdb_000029ly

X-RAY DIFFRACTION

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	29LI

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	0.06 M Divalents : 0.3M Magnesium chloride hexahydrate; 0.3M Calcium chloride dihydrate 0.1 M Imidazole; MES monohydrate (acid) pH 6.5 37.5% v/v Mix 4: 25% v/v MPD; 25% PEG 1000; 25% w/v PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
1.66	25.81

Symmetry
Space Group	P 21 21 21

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 EIGER X 16M		2022-06-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.9762	PETRA III, EMBL c/o DESY	P13 (MX1)

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.2	45.18	100	0.109	0.113	0.032	0.995	15.4	12.5		30092

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.2	1.26		100	0.235	0.245	0.069	0.98		12.2

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.2	36.94	28521	1507	99.95	0.1376	0.13662	0.1436	0.15597	0.1595	RANDOM	13.14

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]
0.04			0.14		-0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.504
r_long_range_B_refined	12.43
r_long_range_B_other	11.838
r_dihedral_angle_2_deg	8.797
r_scangle_other	8.279
r_mcangle_other	5.823
r_mcangle_it	5.817
r_scbond_it	5.752
r_scbond_other	5.748
r_dihedral_angle_1_deg	5.601

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.504
r_long_range_B_refined	12.43
r_long_range_B_other	11.838
r_dihedral_angle_2_deg	8.797
r_scangle_other	8.279
r_mcangle_other	5.823
r_mcangle_it	5.817
r_scbond_it	5.752
r_scbond_other	5.748
r_dihedral_angle_1_deg	5.601
r_mcbond_it	4.016
r_mcbond_other	3.977
r_rigid_bond_restr	3.886
r_angle_refined_deg	1.508
r_angle_other_deg	0.601
r_chiral_restr	0.362
r_bond_refined_d	0.014
r_gen_planes_refined	0.011
r_gen_planes_other	0.003
r_bond_other_d	0.001
r_dihedral_angle_4_deg
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_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	961
Nucleic Acid Atoms
Solvent Atoms	99
Heterogen Atoms	25

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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.