Experiment: 1YAR

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PMA	PDB entry 1PMA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.2	273	0.1M Na-citrate/phosphate buffer, 0.2M Lithium Sulfate, 15% PEG-1000, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
3.4	63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 254.874	α = 90
b = 127.512	β = 92.45
c = 181.182	γ = 90

Symmetry
Space Group	C 1 2 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		2004-02-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X25	1.283	NSLS	X25

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	20	97.4	0.063	0.063	10	5		442007

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	1.9	1.97	95.8		0.497	2.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1PMA	1.9	47.3	442001	440656	1345	97.24	0.18196	0.18196	0.18185	0.21624	RANDOM	31.532

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]
		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.69
r_dihedral_angle_4_deg	14.903
r_dihedral_angle_3_deg	14.644
r_dihedral_angle_1_deg	5.807
r_scangle_it	3.898
r_scbond_it	2.472
r_mcangle_it	1.51
r_angle_refined_deg	1.271
r_mcbond_it	0.973
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.69
r_dihedral_angle_4_deg	14.903
r_dihedral_angle_3_deg	14.644
r_dihedral_angle_1_deg	5.807
r_scangle_it	3.898
r_scbond_it	2.472
r_mcangle_it	1.51
r_angle_refined_deg	1.271
r_mcbond_it	0.973
r_nbtor_refined	0.3
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.167
r_symmetry_vdw_refined	0.161
r_symmetry_hbond_refined	0.149
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	34692
Nucleic Acid Atoms
Solvent Atoms	3470
Heterogen Atoms	147

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.