Experiment: 1PKD

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QMZ	PDB ENTRY 1QMZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.4	277	1.25M (NH4)2SO4, 0.8M KCl, 100mM HEPES, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.88	57.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.62	α = 90
b = 134.57	β = 90
c = 147.97	γ = 90

Symmetry
Space Group	P 21 21 21

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			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1	0.934	ESRF	ID14-1

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	2.3	100	87.8	0.09	4.3		65518	57525

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.38	80.8		0.331	2.6

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 1QMZ	2.3	100	57525	54590	2904	87.03	0.21818	0.21818	0.2155	0.26831	RANDOM	42.484

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]
-0.76			0.81		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.824
r_scangle_it	3.079
r_scbond_it	1.765
r_mcangle_it	1.598
r_angle_refined_deg	1.54
r_mcbond_it	0.844
r_symmetry_vdw_refined	0.311
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.215
r_xyhbond_nbd_refined	0.162

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.824
r_scangle_it	3.079
r_scbond_it	1.765
r_mcangle_it	1.598
r_angle_refined_deg	1.54
r_mcbond_it	0.844
r_symmetry_vdw_refined	0.311
r_nbd_refined	0.218
r_symmetry_hbond_refined	0.215
r_xyhbond_nbd_refined	0.162
r_chiral_restr	0.095
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8942
Nucleic Acid Atoms
Solvent Atoms	402
Heterogen Atoms	72

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	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.