8P8H | pdb_00008p8h

Crystal structure of HHD2 domain of hRTEL1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	AF-Q9NZ71-F1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.1 M CHES pH 9.5, 30% PEG 3000

Crystal Properties
Matthews coefficient	Solvent content
2.13	42.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.59	α = 90
b = 60.68	β = 96.13
c = 79.53	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	PIXEL	DECTRIS PILATUS 6M		2021-11-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	1.0	ELETTRA	11.2C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.3	50	97.9	0.997	10.53	6		27255

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.44	96.2		0.836	1.99

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	FREE R-VALUE	2.3	48.14	27249	1363	97.849	0.216	0.2142	0.22	0.257	0.25	47.233

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]
1.476		1.373	-0.901		-0.85

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.234
r_dihedral_angle_3_deg	15.476
r_dihedral_angle_2_deg	9.701
r_lrange_it	6.576
r_lrange_other	6.576
r_dihedral_angle_1_deg	5.116
r_scangle_it	4.176
r_scangle_other	4.175
r_mcangle_it	3.402
r_mcangle_other	3.402
r_scbond_it	2.669
r_scbond_other	2.669
r_mcbond_it	2.235
r_mcbond_other	2.232
r_angle_refined_deg	1.887
r_angle_other_deg	0.624
r_symmetry_xyhbond_nbd_refined	0.266
r_nbd_refined	0.249
r_nbd_other	0.199
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.184
r_symmetry_nbd_refined	0.175
r_xyhbond_nbd_refined	0.129
r_ncsr_local_group_9	0.113
r_ncsr_local_group_18	0.112
r_ncsr_local_group_16	0.11
r_ncsr_local_group_7	0.109
r_ncsr_local_group_12	0.107
r_ncsr_local_group_1	0.104
r_ncsr_local_group_20	0.104
r_ncsr_local_group_3	0.103
r_ncsr_local_group_19	0.103
r_ncsr_local_group_4	0.1
r_ncsr_local_group_11	0.099
r_ncsr_local_group_13	0.098
r_ncsr_local_group_2	0.096
r_ncsr_local_group_10	0.095
r_ncsr_local_group_17	0.095
r_ncsr_local_group_5	0.092
r_chiral_restr	0.087
r_ncsr_local_group_8	0.082
r_ncsr_local_group_15	0.082
r_ncsr_local_group_6	0.08
r_symmetry_nbtor_other	0.075
r_ncsr_local_group_21	0.073
r_ncsr_local_group_14	0.067
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4188
Nucleic Acid Atoms
Solvent Atoms	60
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing