2Z5R | pdb_00002z5r

Apo-Fr with high content of Pd ions

X-RAY DIFFRACTION

---

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Ammonium sulfate, Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 181.594	α = 90
b = 181.594	β = 90
c = 181.594	γ = 90

Symmetry
Space Group	F 4 3 2

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 315		2006-03-03	M	SINGLE WAVELENGTH
2	1	100	CCD	ADSC QUANTUM 315		2006-03-03

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.5086	SPring-8	BL41XU
2	SYNCHROTRON	SPRING-8 BEAMLINE BL41XU	0.4639	SPring-8	BL41XU

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	2.5	50	100	0.092	33.9	11.6		9397		-3	39.084

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)
	2.5	2.69	100		0.302	7.2	11.8

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	1DAT	2.5	45.41	8894	503	99.96	0.22298	0.21943	0.21	0.28671	0.28	RANDOM	31.593

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.964
r_dihedral_angle_4_deg	27.738
r_dihedral_angle_3_deg	21.981
r_sphericity_free	19.109
r_dihedral_angle_1_deg	11.829
r_scangle_it	6.356
r_scbond_it	4.155
r_mcangle_it	2.451
r_angle_refined_deg	2.262
r_mcbond_it	1.495
r_nbtor_refined	0.315
r_symmetry_hbond_refined	0.307
r_metal_ion_refined	0.305
r_nbd_refined	0.274
r_symmetry_vdw_refined	0.225
r_chiral_restr	0.202
r_xyhbond_nbd_refined	0.162
r_bond_refined_d	0.026
r_gen_planes_refined	0.01
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1366
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	12

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
SCALEPACK	data scaling
MOLREP	phasing