5HZU | pdb_00005hzu

Crystal structure of Dronpa-Ni2+

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2GX2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	295.5	PEG 4000, Tris-HCl, MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 105.372	α = 71.11
b = 109.403	β = 85.97
c = 72.087	γ = 61.3

Symmetry
Space Group	P 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	ADSC QUANTUM 210		2013-12-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PAL/PLS BEAMLINE 7A (6B, 6C1)	1.0	PAL/PLS	7A (6B, 6C1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.89	30	94.9	22.185	3		198444

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 (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	2GX2	1.89	29.03	188475	9967	93.96	0.1534	0.1509	0.16	0.1993	0.21	RANDOM	24.27

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]
-0.75	0.11	-0.04	-0.49	-0.19	1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.051
r_dihedral_angle_3_deg	14.707
r_dihedral_angle_4_deg	14.526
r_dihedral_angle_1_deg	7.167
r_mcangle_it	2.799
r_angle_refined_deg	2.064
r_mcbond_it	2.038
r_mcbond_other	2.035
r_angle_other_deg	0.893
r_chiral_restr	0.124

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.051
r_dihedral_angle_3_deg	14.707
r_dihedral_angle_4_deg	14.526
r_dihedral_angle_1_deg	7.167
r_mcangle_it	2.799
r_angle_refined_deg	2.064
r_mcbond_it	2.038
r_mcbond_other	2.035
r_angle_other_deg	0.893
r_chiral_restr	0.124
r_bond_refined_d	0.02
r_gen_planes_refined	0.011
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	20706
Nucleic Acid Atoms
Solvent Atoms	2004
Heterogen Atoms	25

Software

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

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.