3FI6

apo-H49AFr with high content of Pd ions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1DAT	PDB ENTRY 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
3.11	60.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 180.701	α = 90
b = 180.701	β = 90
c = 180.701	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	RIGAKU JUPITER 210		2008-11-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL38B1	1.0	SPring-8	BL38B1

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	30	100	0.089	57.4	11.6		24004

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	100		0.3	8	11.4

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 ENTRY 1DAT	1.8	21.3	22765	1228	99.95	0.19712	0.19566	0.22526	RANDOM	20.797

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	35.17
r_dihedral_angle_4_deg	23.442
r_dihedral_angle_3_deg	14.917
r_dihedral_angle_1_deg	4.706
r_scangle_it	3.742
r_scbond_it	2.46
r_mcangle_it	1.468
r_angle_refined_deg	1.252
r_mcbond_it	0.996
r_nbtor_refined	0.303
r_nbd_refined	0.23
r_symmetry_vdw_refined	0.204
r_metal_ion_refined	0.168
r_xyhbond_nbd_refined	0.159
r_symmetry_hbond_refined	0.159
r_symmetry_metal_ion_refined	0.121
r_chiral_restr	0.094
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1406
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	14

Software

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