6YDV | pdb_00006ydv

Crystal Structure of the Jmjc Domain of Human JMJD1B in complex with FM001511a from the DSPL fragment library

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6RBJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	277	0.1M bis-tris pH 5.5, 24% PEG3350, 0.4M magnesium chloride

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.58

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.6	α = 90
b = 93.79	β = 107.5
c = 92.61	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 2M		2015-09-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9282	Diamond	I02

Data Collection

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	2.07	54.934	99.2	0.085	0.13	0.069	0.996	10.2	3.4		56778			32.041

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.07	9.26	99.1		0.961	0.713	0.556	1.3	3.5

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	6RBJ	2.07	54.934	56756	2774	99.122	0.172	0.1696	0.18	0.2137	0.22	40.58

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]
3.129		0.238	-3.372		0.077

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.67
r_dihedral_angle_4_deg	15.386
r_dihedral_angle_3_deg	14.616
r_dihedral_angle_1_deg	7.205
r_lrange_it	3.484
r_lrange_other	3.169
r_scangle_it	2.572
r_scangle_other	2.571
r_mcangle_it	2.465
r_mcangle_other	2.465
r_scbond_it	2.281
r_scbond_other	2.28
r_mcbond_it	2.147
r_mcbond_other	2.137
r_angle_refined_deg	1.309
r_angle_other_deg	1.233
r_rigid_bond_restr	0.688
r_symmetry_xyhbond_nbd_refined	0.482
r_nbd_other	0.192
r_nbd_refined	0.183
r_symmetry_nbd_other	0.183
r_nbtor_refined	0.154
r_xyhbond_nbd_refined	0.139
r_symmetry_nbd_refined	0.129
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.059
r_gen_planes_refined	0.005
r_bond_refined_d	0.004
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5506
Nucleic Acid Atoms
Solvent Atoms	629
Heterogen Atoms	22

Software

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