Experiment: 1YQO

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6	277	100mM sodium PIPES, 40mM MgSO4, 18-21% PEG8000, pH 6.0-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.727	α = 90
b = 152.962	β = 94.37
c = 61.732	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	ADSC QUANTUM 4		2003-05-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.1	0.9831	SRS	PX14.1

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	1.9	24	99.4	0.043	33.4			84625

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)
	1.9	1.97	94.8		0.144	7.95		8015

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	PDB ID 2HPD	1.9	24	80366	4224	99.36	0.16842	0.16639	0.17	0.20635	0.21	RANDOM	25.22

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]
-0.93		1.05	-0.68		1.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.815
r_dihedral_angle_4_deg	16.613
r_dihedral_angle_3_deg	14.919
r_dihedral_angle_1_deg	6.428
r_scangle_it	4.503
r_scbond_it	3.022
r_mcangle_it	1.81
r_angle_refined_deg	1.696
r_mcbond_it	1.212
r_nbtor_refined	0.313

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.815
r_dihedral_angle_4_deg	16.613
r_dihedral_angle_3_deg	14.919
r_dihedral_angle_1_deg	6.428
r_scangle_it	4.503
r_scbond_it	3.022
r_mcangle_it	1.81
r_angle_refined_deg	1.696
r_mcbond_it	1.212
r_nbtor_refined	0.313
r_symmetry_vdw_refined	0.229
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.212
r_xyhbond_nbd_refined	0.197
r_chiral_restr	0.131
r_bond_refined_d	0.02
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7058
Nucleic Acid Atoms
Solvent Atoms	986
Heterogen Atoms	86

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

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.