9O4Y | pdb_00009o4y

GAS41 YEATS domain in complex with DLG-1

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277	1260 mM Ammonium sulfate, 100 mM HEPES, pH 7.5, 25% Glycerol

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.32

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 68.499	α = 90
b = 62.619	β = 93.342
c = 84.029	γ = 90

Symmetry
Space Group	P 1 21 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 300 mm CCD		2019-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	2.3	50	99.6	0.098	24.98	3.6		31700

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34			0.598	2.04	3.4

Refinement

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.3	41.978	31687	1487	99.332	0.199	0.1965	0.2002	0.2576	0.2585	56.701

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]
4.568		-2.627	-4.961		0.694

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.191
r_dihedral_angle_3_deg	13.522
r_lrange_other	12.481
r_lrange_it	12.48
r_dihedral_angle_2_deg	11.508
r_scangle_it	9.171
r_scangle_other	9.17
r_mcangle_other	8.173
r_mcangle_it	8.172
r_dihedral_angle_1_deg	7.585
r_scbond_it	6.245
r_scbond_other	6.244
r_mcbond_it	5.726
r_mcbond_other	5.698
r_dihedral_angle_other_2_deg	5.637
r_angle_refined_deg	1.881
r_angle_other_deg	0.553
r_symmetry_nbd_other	0.196
r_nbd_refined	0.193
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.179
r_nbd_other	0.146
r_symmetry_nbd_refined	0.136
r_symmetry_nbtor_other	0.091
r_symmetry_xyhbond_nbd_refined	0.078
r_chiral_restr	0.07
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	3962
Nucleic Acid Atoms
Solvent Atoms	141
Heterogen Atoms	172

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing