Experiment: 1YQP

X-RAY DIFFRACTION

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	51.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.876	α = 90
b = 153.241	β = 94.48
c = 61.607	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		2004-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX14.2	1.488	SRS	PX14.2

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	1.8	24	99.4	0.091	10.1			99832

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)
	1.8	1.86	99.8		0.348	3.56		10017

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ID 2HPD	1.8	24	94797	4991	99.44	0.17617	0.17439	0.21019	RANDOM	26.602

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]
-1.19		0.73	-0.74		2.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.918
r_dihedral_angle_4_deg	16.482
r_dihedral_angle_3_deg	15.103
r_dihedral_angle_1_deg	6.294
r_scangle_it	4.366
r_scbond_it	2.891
r_mcangle_it	1.751
r_angle_refined_deg	1.666
r_mcbond_it	1.175
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.918
r_dihedral_angle_4_deg	16.482
r_dihedral_angle_3_deg	15.103
r_dihedral_angle_1_deg	6.294
r_scangle_it	4.366
r_scbond_it	2.891
r_mcangle_it	1.751
r_angle_refined_deg	1.666
r_mcbond_it	1.175
r_nbtor_refined	0.311
r_nbd_refined	0.22
r_symmetry_vdw_refined	0.196
r_symmetry_hbond_refined	0.194
r_xyhbond_nbd_refined	0.173
r_chiral_restr	0.125
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7044
Nucleic Acid Atoms
Solvent Atoms	973
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 National Science Foundation (DBI-1832184), 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 R01GM133198.