Experiment: 3HJM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3CSI	PDB ENTRY 3CSI

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.4	298	270mM Calcium Acetate, 20% PEG8000, 100mM MES, pH5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.53	51.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.002	α = 90
b = 90.393	β = 97.49
c = 75.981	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	IMAGE PLATE	RIGAKU RAXIS IV++	AXCO	2008-08-15	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 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	2.1	54.55	98.8	0.11	0.11	6.26	5.7		53439			21.99

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)
	2.1	2.21	92.1		0.41	0.41	1.8	4.8	7215

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 3CSI	2.1	54.55	53417	2735	98.85	0.18	0.18	0.23	RANDOM	21.361

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]
-1.25		-1.16	-1.09		2.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.298
r_dihedral_angle_4_deg	16.094
r_dihedral_angle_3_deg	13.993
r_dihedral_angle_1_deg	5.78
r_scangle_it	3.101
r_scbond_it	2.033
r_angle_refined_deg	1.489
r_mcangle_it	1.236
r_mcbond_it	0.781
r_nbtor_refined	0.301

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.298
r_dihedral_angle_4_deg	16.094
r_dihedral_angle_3_deg	13.993
r_dihedral_angle_1_deg	5.78
r_scangle_it	3.101
r_scbond_it	2.033
r_angle_refined_deg	1.489
r_mcangle_it	1.236
r_mcbond_it	0.781
r_nbtor_refined	0.301
r_nbd_refined	0.197
r_symmetry_vdw_refined	0.171
r_xyhbond_nbd_refined	0.156
r_metal_ion_refined	0.117
r_symmetry_hbond_refined	0.116
r_chiral_restr	0.096
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6509
Nucleic Acid Atoms
Solvent Atoms	621
Heterogen Atoms	69

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
PHASER	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.