Experiment: 3P4U

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293	0.05 M calcium acetate, 0.1 M sodium cacodylate pH 5.5 and 12% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.05	40.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.455	α = 90
b = 89.5	β = 111.73
c = 61.245	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	RIGAKU SATURN 944			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF	1.54

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	19.904	92.1	0.102	13.6	6	40267	40267

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	2	68.7		0.313	0.313	2.4	4.5	4362

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.9	19.9	40238	2030	91.95	0.1514	0.1496	0.1854	RANDOM	10.7916

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]
-0.23		0.12	0.35		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.295
r_dihedral_angle_4_deg	15.526
r_dihedral_angle_3_deg	11.534
r_dihedral_angle_1_deg	5.943
r_scangle_it	2.182
r_scbond_it	1.303
r_angle_refined_deg	1.05
r_angle_other_deg	0.785
r_mcangle_it	0.781
r_mcbond_it	0.393

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.295
r_dihedral_angle_4_deg	15.526
r_dihedral_angle_3_deg	11.534
r_dihedral_angle_1_deg	5.943
r_scangle_it	2.182
r_scbond_it	1.303
r_angle_refined_deg	1.05
r_angle_other_deg	0.785
r_mcangle_it	0.781
r_mcbond_it	0.393
r_chiral_restr	0.076
r_mcbond_other	0.075
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3879
Nucleic Acid Atoms
Solvent Atoms	613
Heterogen Atoms

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection

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.